Re: [gmx-users] Ligand in PRODRG server is protonated. Why?

[Justin Lemkul]

On 2/14/20 11:13 AM, Andrew Bostick wrote:

Dear gromacs users,

I am doing MD simulation of protein-ligand complex. For ligand, I used
PRODRG server.

My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of
Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In
PRODRG outputs, ligand is protonated on N atom and has 1 atom more than
original structure (58 atoms). I don't want this output. My aim is studying
unprotonated structure of Tamoxifen.

How to resolve that.


Protonation is addressed in their FAQ: 
http://prodrg1.dyndns.org/prodrg_faq.html


I strongly discourage you from using PRODRG. Its topologies are of 
inadequate quality for MD simulations and were never intended to be used 
for such.


-Justin

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Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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[gmx-users] Ligand in PRODRG server is protonated. Why?

[Andrew Bostick]

Dear gromacs users,

I am doing MD simulation of protein-ligand complex. For ligand, I used
PRODRG server.

My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of
Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In
PRODRG outputs, ligand is protonated on N atom and has 1 atom more than
original structure (58 atoms). I don't want this output. My aim is studying
unprotonated structure of Tamoxifen.

How to resolve that.

Best,
Andrew
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Re: [gmx-users] ligand topology building.

[Justin Lemkul]

On 11/4/19 2:07 AM, Yogesh Sharma wrote:

hello users

I am using ATB server for ligand topology development.  there is a section
named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP  what
does it mean? and in  files section there is choice  for Topology Files and
structure files as following

GROMACS G54A7FF All-Atom (ITP file)

GROMACS G54A7FF United-Atom (ITP file)

Structure Files

All-Atom PDB (optimised geometry)

United-Atom PDB (optimised geometry)

United-Atom PDB (original geometry)

All-Atom PDB (original geometry)

  what are the best option to proceed with, avoiding artifacts?


Is GROMOS a united-atom or all-atom force field?

-Justin

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==

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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] ligand topology building.

[Yogesh Sharma]

hello users

I am using ATB server for ligand topology development.  there is a section
named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP  what
does it mean? and in  files section there is choice  for Topology Files and
structure files as following

GROMACS G54A7FF All-Atom (ITP file)

GROMACS G54A7FF United-Atom (ITP file)

Structure Files

All-Atom PDB (optimised geometry)

United-Atom PDB (optimised geometry)

United-Atom PDB (original geometry)

All-Atom PDB (original geometry)

 what are the best option to proceed with, avoiding artifacts?

Thank you for your time.
 *  with  regards*
*Yogesh Sharma*
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[gmx-users] ligand topology building

[Yogesh Sharma]

hello users

I am using ATB server for ligand topology development.  there is a section
named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP  what
does it mean? and in  files section there is choice  for Topology Files and
structure files as following

GROMACS G54A7FF All-Atom (ITP file)

GROMACS G54A7FF United-Atom (ITP file)

Structure Files

All-Atom PDB (optimised geometry)

United-Atom PDB (optimised geometry)

United-Atom PDB (original geometry)

All-Atom PDB (original geometry)

 what are the best option to proceed with, avoiding artifacts?

Thank you for your time.
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Re: [gmx-users] Ligand molecule occupancy

[Justin Lemkul]

On 9/25/19 5:46 AM, Pandya, Akash wrote:

Hi,

I have multiple ligand molecules of the same type in my system. If I wanted to 
monitor the Cartesian coordinates of each individual ligand during a 
simulation, is there a Gromacs tool to do that? or do I have write a custom 
script?


You can print coordinates over time using gmx traj.

-Justin


Some background:
My purpose is to look at binding/unbinding events for each ligand individually. 
I have calculated the minimum distance between protein residues and ligands in 
my system, but this does not give the identity of the ligand (e.g. resid or 
atom number) within a particular cut-off. I used the gmx pairdist module in 
Gromacs to calculate the minimum distance.

Any guidance will be much appreciated.

Best wishes,

Akash


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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[gmx-users] Ligand molecule occupancy

[Pandya, Akash]

Hi,

I have multiple ligand molecules of the same type in my system. If I wanted to 
monitor the Cartesian coordinates of each individual ligand during a 
simulation, is there a Gromacs tool to do that? or do I have write a custom 
script?

Some background:
My purpose is to look at binding/unbinding events for each ligand individually. 
I have calculated the minimum distance between protein residues and ligands in 
my system, but this does not give the identity of the ligand (e.g. resid or 
atom number) within a particular cut-off. I used the gmx pairdist module in 
Gromacs to calculate the minimum distance.

Any guidance will be much appreciated.

Best wishes,

Akash
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Re: [gmx-users] ligand in water

[Bratin Kumar Das]

Hi
The procedure you are following is not ok. Generate the co-ordinate
file of ligand and the topology parameter file. Setup the box and add water
to it. Lastly do energy minimisation.

On Thu 9 May, 2019, 2:33 PM RAHUL SURESH,  wrote:

> Hi Users.
>
> I want to simulate ligand in the water box. I prepared a water molecule and
> started with pdb2gmx and then planned to follow protein-ligand tutorial.
> Unfortunately ended up with an error in gro file format. Have check every
> possibility but still couldn't find any solution.
> My initial pdb is water.pdb and the corresponding gro file is water.gro. I
> clubbed the ligand gro file and water gro file as complex.gro. I have
> uploaded the file here. can anyone help me with the format issues>?
>
> --
> *Regards,*
> *Rahul *
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Re: [gmx-users] ligand in water

[Dallas Warren]

This will do it (if need particular water model change with cs switch
options, and assumes ligand.gro has the correct final box size)

gmx solvate - cp ligand.gro -cs -o complex.gro

Unless you have a particular number of waters required, then use.:

gmx solvate - cp ligand.gro -cs -o complex.gro -maxsol 

To both above add -p topol.top if want it to automatically update the
topology file with number of molecules/residues. Otherwise you need to do
by hand, which is easy enough.

Or even if need a particular water coordinate file:

gmx insert-molecules -f ligand.gro -ci water.gro -nmol  -o complex.gro

On Thu, 9 May 2019, 7:02 pm RAHUL SURESH,  wrote:

> Hi Users.
>
> I want to simulate ligand in the water box. I prepared a water molecule and
> started with pdb2gmx and then planned to follow protein-ligand tutorial.
> Unfortunately ended up with an error in gro file format. Have check every
> possibility but still couldn't find any solution.
> My initial pdb is water.pdb and the corresponding gro file is water.gro. I
> clubbed the ligand gro file and water gro file as complex.gro. I have
> uploaded the file here. can anyone help me with the format issues>?
>
> --
> *Regards,*
> *Rahul *
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[gmx-users] ligand in water

[RAHUL SURESH]

Hi Users.

I want to simulate ligand in the water box. I prepared a water molecule and
started with pdb2gmx and then planned to follow protein-ligand tutorial.
Unfortunately ended up with an error in gro file format. Have check every
possibility but still couldn't find any solution.
My initial pdb is water.pdb and the corresponding gro file is water.gro. I
clubbed the ligand gro file and water gro file as complex.gro. I have
uploaded the file here. can anyone help me with the format issues>?

-- 
*Regards,*
*Rahul *
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Re: [gmx-users] ligand-polymer interaction in triclinic unit cell

[Dallas Warren]

1/ as long as the frame within the .tpr file or first frame within the .xtc
file fed to trjconv has the molecules/particles as shown in figure 1, then
it should maintain them as such, even if they diffuse away.  I'd recheck
what you have done there.

2/ periodic_molecules is for molecules that cross the PBC boundary,
typically those that are a single long chain that links back to itself at
the other end.
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=periodic%20molecules#mdp-periodic-molecules.
The box you are visualising doen't actually exist within the simulation, it
is an artificial construct so that you can look at it. And you can place
that box where ever you like.  What is important is the relative
positioning of the molecules to each other, and whether that is valid with
respect to what you are studying.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 8 Feb 2019 at 11:36, Wei-Ta Li  wrote:

> Hello everyone,
>
> I am trying to simulate interaction of polymer with ligand. The polymer is
> represented by infinite sheet build by propagation in 2 dimensions of
> monomer obtained from crystal structure. Since the polymer was crystallized
> in triclinic unit cell, the propagation of the sheet also appears to be
> triclinic. The topology was obtained by "gmx x2top ... -pbc". The schematic
> representation of the  structure before simulation is shown below where the
> monomer units are *, L is the ligand, \ are boundaries of the unit cell and
> water is omitted for the sake of simplicity:
>
> \\
>  \ \
>   \ \
>\ \
> \   L \
>  \  \
>   \  \
>\**\
> \**\
>  \**\
>
> System was simulated with typical parameters and "pbc = xyz",
> "periodic_molecules = yes" flags. After extraction of trajectory with "gmx
> trjconv -s whatever.tpr -f whatever.trr -o whatever.pdb -pbc nojump -dt
> 10", the structure looks like scheme below:
>
> \\  **
>  \\  *
>   \\
>\ \
> \   L\
>  \ \
>   \  \
>\  \
> \ *\
>  \**\
>
> From Gromacs manual I understand that such representation is expected
> because regardless of the input box shape the simulation proceeds in the
> brick-shape form: "Even when simulating using a triclinic box, GROMACS
> always keeps the particles in a brick-shaped volume for efficiency, as
> illustrated in Fig. 3.1 for a 2-dimensional system". Nonetheless I have 2
> questions:
>
> 1) Why "-pbc nojump" processing does not result in the representation like
> in Scheme_1? Shouldn't it put the atoms back in the original box like
> stated in the description: "nojump checks if atoms jump across the box and
> then puts them back"? Or does it mean brick-shaped box which Gromacs uses
> for simulation? Is there other way to have representation after simulation
> as in scheme 1?
>
> 2) Second question is somewhat naive, but nonetheless. Is such skewed
> representation of the polymer sheet valid for simulation set up? In other
> words, does this "skewness" have effect on polymer-ligand interaction? In
> the brick shaped representation the left side has 3 layers, but the right
> is gradual ladder-like increase of layers from 1 to 3, and then there is a
> fragment of polymer on top of the box. Does the setting "periodic_molecules
> = yes" take care of it?
>
> Thanks in advance!
> Wei-Ta Li
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[gmx-users] ligand-polymer interaction in triclinic unit cell

[Wei-Ta Li]

Hello everyone,

I am trying to simulate interaction of polymer with ligand. The polymer is
represented by infinite sheet build by propagation in 2 dimensions of
monomer obtained from crystal structure. Since the polymer was crystallized
in triclinic unit cell, the propagation of the sheet also appears to be
triclinic. The topology was obtained by "gmx x2top ... -pbc". The schematic
representation of the  structure before simulation is shown below where the
monomer units are *, L is the ligand, \ are boundaries of the unit cell and
water is omitted for the sake of simplicity:

\\
 \ \
  \ \
   \ \
\   L \
 \  \
  \  \
   \**\
\**\
 \**\

System was simulated with typical parameters and "pbc = xyz",
"periodic_molecules = yes" flags. After extraction of trajectory with "gmx
trjconv -s whatever.tpr -f whatever.trr -o whatever.pdb -pbc nojump -dt
10", the structure looks like scheme below:

\\  **
 \\  *
  \\
   \ \
\   L\
 \ \
  \  \
   \  \
\ *\
 \**\

>From Gromacs manual I understand that such representation is expected
because regardless of the input box shape the simulation proceeds in the
brick-shape form: "Even when simulating using a triclinic box, GROMACS
always keeps the particles in a brick-shaped volume for efficiency, as
illustrated in Fig. 3.1 for a 2-dimensional system". Nonetheless I have 2
questions:

1) Why "-pbc nojump" processing does not result in the representation like
in Scheme_1? Shouldn't it put the atoms back in the original box like
stated in the description: "nojump checks if atoms jump across the box and
then puts them back"? Or does it mean brick-shaped box which Gromacs uses
for simulation? Is there other way to have representation after simulation
as in scheme 1?

2) Second question is somewhat naive, but nonetheless. Is such skewed
representation of the polymer sheet valid for simulation set up? In other
words, does this "skewness" have effect on polymer-ligand interaction? In
the brick shaped representation the left side has 3 layers, but the right
is gradual ladder-like increase of layers from 1 to 3, and then there is a
fragment of polymer on top of the box. Does the setting "periodic_molecules
= yes" take care of it?

Thanks in advance!
Wei-Ta Li
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[gmx-users] ligand dissociation in gromacs

[venkat]

Sir,
  i need to study Crystal complex structure (protein and ligand)
ligand dissociation by using md methods.  Is there any way perform in
gromacs like RAMD
if its there means kindly provide tutorial for that it will helpful for me.

Thank You.

Sincerely
S.venkatesh
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Re: [gmx-users] ligand itp file doesn't have dihedral angles that including H atom

[Mark Abraham]

Hi,

They are presumably looked up from the parameters found normally in the
force field files.

Mark

On Wed, Jan 3, 2018 at 6:22 PM MD  wrote:

> Hi Gromacs folks,
>
> I noticed the topology file of ligand from atb site doesn't have dihedral
> angles that include H. Do you know how to create a itp file that has
> hydrogen included dihedral parameters?
>
> Thanks,
>
> Ming
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[gmx-users] ligand itp file doesn't have dihedral angles that including H atom

[MD]

Hi Gromacs folks,

I noticed the topology file of ligand from atb site doesn't have dihedral
angles that include H. Do you know how to create a itp file that has
hydrogen included dihedral parameters?

Thanks,

Ming
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Re: [gmx-users] ligand

[‪farial tavakoli‬ ‪]

Hi Justin 

Thank you so much
with best 
Farial


  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Monday, 14 August 2017, 16:35:58
 Subject: Re: [gmx-users] ligand
   


On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
> Thanks for your advice.Now I am trying to create a .gro file from the united 
> atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
> xxx.gro
> but faced to this warning:
> WARNING: all CONECT records are ignored
> would you please advice me how can i solve this problem?

You don't.  You don't need connectivity information from the PDB because 
it's all in the topology.  This really shouldn't be a "warning," rather 
an informative note.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }   Dear justin
Thank you so much 
Yours sincerelyFarial


Sent from Yahoo Mail for iPhone


On Monday, August 14, 2017, 4:35 PM, Justin Lemkul  wrote:



On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear Justin
> Thanks for your advice.Now I am trying to create a .gro file from the united 
> atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
> xxx.gro
> but faced to this warning:
> WARNING: all CONECT records are ignored
> would you please advice me how can i solve this problem?

You don't.  You don't need connectivity information from the PDB because 
it's all in the topology.  This really shouldn't be a "warning," rather 
an informative note.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] ligand

[Justin Lemkul]

On 8/14/17 2:03 AM, ‪farial tavakoli‬ ‪ wrote:

Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united 
atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would you please advice me how can i solve this problem?


You don't.  You don't need connectivity information from the PDB because 
it's all in the topology.  This really shouldn't be a "warning," rather 
an informative note.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] ligand

[‪farial tavakoli‬ ‪]

Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united 
atom pdb structure file obtained from ATB  by using :editconf -f xxx.pdb -o 
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would you please advice me how can i solve this problem?
thanks alotFarial

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Sunday, 13 August 2017, 21:45:53
 Subject: Re: [gmx-users] ligand
   


On 8/13/17 12:29 PM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
>#715FFA solid !important; padding-left:1ex !important; background-color:white 
>!important; }  Dear justin
> Thank you for your replyI thought that topology file obtained from ATB needs 
> to be changed like PRODRG
> 

No, they generally should not.  ATB is a much better topology source than 
PRODRG.  That doesn't necessarily mean you should always trust a black box 
without some validation, but you shouldn't just blindly go messing with things 
because some other program is known to be problematic.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] ligand

[Justin Lemkul]

On 8/13/17 12:29 PM, farial tavakoli wrote:

  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
Thank you for your replyI thought that topology file obtained from ATB needs to 
be changed like PRODRG



No, they generally should not.  ATB is a much better topology source than 
PRODRG.  That doesn't necessarily mean you should always trust a black box 
without some validation, but you shouldn't just blindly go messing with things 
because some other program is known to be problematic.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] ligand

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear justin
Thank you for your replyI thought that topology file obtained from ATB needs to 
be changed like PRODRG


Sent from Yahoo Mail for iPhone


On Sunday, August 13, 2017, 8:43 PM, Justin Lemkul  wrote:



On 8/13/17 3:13 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear GROMACS users
> 
> I noticed my ligand has some broken bonds and changes in atoms arrengement 
> after md simulation was done. I have read before that no bond is broken and 
> created in simulation . So why have been ligand changed ?
> I think, i have to notice that when i wanted to create a ligand topology , i 
> used ATB server to create topology and pdb files. and when wanted to reassign 
> the charges and charge groups, noticed that some of the atoms of ligand that 
> have to be in a charge group, were not successive  , so decided to rearrange 
> them and replaced them to place them in a charge group.

Why did you modify the topology?  Usually ATB topologies require no 
modification.  If you "rearranged" atoms in any way, then you irreparably broke 
the topology because no all of the bonded interactions are nonsense.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] ligand

[Justin Lemkul]

On 8/13/17 3:13 AM, ‪farial tavakoli‬ ‪ wrote:

Dear GROMACS users

I noticed my ligand has some broken bonds and changes in atoms arrengement 
after md simulation was done. I have read before that no bond is broken and 
created in simulation . So why have been ligand changed ?
I think, i have to notice that when i wanted to create a ligand topology , i 
used ATB server to create topology and pdb files. and when wanted to reassign 
the charges and charge groups, noticed that some of the atoms of ligand that 
have to be in a charge group, were not successive  , so decided to rearrange 
them and replaced them to place them in a charge group.


Why did you modify the topology?  Usually ATB topologies require no 
modification.  If you "rearranged" atoms in any way, then you irreparably broke 
the topology because no all of the bonded interactions are nonsense.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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[gmx-users] ligand

[‪farial tavakoli‬ ‪]

Dear GROMACS users

I noticed my ligand has some broken bonds and changes in atoms arrengement 
after md simulation was done. I have read before that no bond is broken and 
created in simulation . So why have been ligand changed ? 
I think, i have to notice that when i wanted to create a ligand topology , i 
used ATB server to create topology and pdb files. and when wanted to reassign 
the charges and charge groups, noticed that some of the atoms of ligand that 
have to be in a charge group, were not successive  , so decided to rearrange 
them and replaced them to place them in a charge group. 
I dont know if it is possible the brocken bonds in the ligand after simulation 
for 1 ns because of its topology?I am using gromacs 2016.3 and gromos96 54 a7 
ff.


thanks in advanceTavakoli

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Re: [gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

I have found

However, if one wants *acpype* just to emulate *amb2gmx.pl*, one needs
nothing
at all but *[http://www.python.org Python]*.

At the moment, *acpype* is only available for download via *svn*:

  * `svn checkout http://acpype.googlecode.com/svn/trunk/ acpype`

Yet, if some reason you cannot use *svn*, one still can get *acpype* with:

  * `wget http://acpype.googlecode.com/svn/trunk/acpype.py`

But be aware that one may run in extra troubles and I am not willing to
support
this way.

== To Test ==

At folder *acpype/test*, type:

  * `../acpype.py -i FFF.pdb`

It'll create a folder called *FFF.acpype*, and inside it one may find
topology
files for GROMACS and CNS/XPLOR.


On Tue, Aug 1, 2017 at 3:00 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Have you read the acpype documentation before trying to use it?
>
> Mark
>
> On Tue, 1 Aug 2017 23:19 Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com>
> wrote:
>
> > Dear Sir
> >
> > I have just use acpype.py -i OAI.pdb
> > I am getting the error:
> > ERROR: no 'antechamber' executable!
> > ERROR: no 'antechamber' executable... aborting !
> > ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> > ==> HINT2: is 'antechamber' in your $PATH?
> > What 'which antechamber' in your terminal says?
> > 'alias' doesn't work for ACPYPE.
> > ACPYPE FAILED: 1
> > Total time of execution: less than a second
> >
> > I am thinking that I have to install amber. But I dont want to do that.
> Is
> > there any way that I can create ligand topology for gaff.
> >
> >
> >
> > On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> > >
> > >> Ok, you should not mix and match forcefields, ¿but in the case of
> > >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> > >>
> > >
> > > GAFF is compatible with AMBER (by design).  My comments were warning
> that
> > > one should not use AMBER for a protein in concert with GROMOS for a
> > ligand.
> > >
> > > -Justin
> > >
> > > Best regards.
> > >> Lucio Montero.
> > >>
> > >> Enviado desde Correo para Windows 10
> > >>
> > >> De: Alan
> > >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> > >> Para: Gromacs
> > >> Asunto: Re: [gmx-users] ligand topology
> > >>
> > >> Please this GitHub link is totally outdated and not linked in any
> sense
> > to
> > >> the original authors.
> > >>
> > >> Get the correct ACPYPE here:
> > >>
> > >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> > >> stable/ccpn/python/acpype acpype
> > >>
> > >> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com>
> wrote:
> > >>
> > >> Actually, GAFF forcefield and amber forcefields are compatible. gaff
> is
> > >>> simply amber ff for small molecules.
> > >>> You have to get first amber tools. The last release is amber tools 16
> > >>> Get the source code from here :
> > >>> http://ambermd.org/AmberTools16-get.html
> > >>>
> > >>> after installation you can use antechamber for creating the
> > >>> small-molecule
> > >>> parameters
> > >>>
> > >>> later, you can use a nice free program called ACEPYP, made to convert
> > >>> amber
> > >>> parameters to gromacs toplogyget the code from here:
> > >>>
> > >>> https://github.com/t-/acpype
> > >>>
> > >>> Regards
> > >>>
> > >>>
> > >>>
> > >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> > >>> za.par...@gmail.com> wrote:
> > >>>
> > >>> Dear Sir
> > >>>>
> > >>>> Thank you very much for your reply. Can you give me any link or
> > >>>>
> > >>> suggestion
> > >>>
> > >>>> that i can learn for amber force field for protein and ligand.
> > >>>>
> > >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu>
> > wrote:
> > >>>>
> > >>>>
> > >>>>>
> > >>>>> On

Re: [gmx-users] ligand topology

[Alan]

http://webapps.ccpn.ac.uk/acpype/

On 1 August 2017 at 22:18, Mohammad Zahidul Hossain Khan <
za.par...@gmail.com> wrote:

> Dear Sir
>
> I have just use acpype.py -i OAI.pdb
> I am getting the error:
> ERROR: no 'antechamber' executable!
> ERROR: no 'antechamber' executable... aborting !
> ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> ==> HINT2: is 'antechamber' in your $PATH?
> What 'which antechamber' in your terminal says?
> 'alias' doesn't work for ACPYPE.
> ACPYPE FAILED: 1
> Total time of execution: less than a second
>
> I am thinking that I have to install amber. But I dont want to do that. Is
> there any way that I can create ligand topology for gaff.
>
>
>
> On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>
> >
> >
> > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> >
> >> Ok, you should not mix and match forcefields, ¿but in the case of
> >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> >>
> >
> > GAFF is compatible with AMBER (by design).  My comments were warning that
> > one should not use AMBER for a protein in concert with GROMOS for a
> ligand.
> >
> > -Justin
> >
> > Best regards.
> >> Lucio Montero.
> >>
> >> Enviado desde Correo para Windows 10
> >>
> >> De: Alan
> >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> >> Para: Gromacs
> >> Asunto: Re: [gmx-users] ligand topology
> >>
> >> Please this GitHub link is totally outdated and not linked in any sense
> to
> >> the original authors.
> >>
> >> Get the correct ACPYPE here:
> >>
> >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> >> stable/ccpn/python/acpype acpype
> >>
> >> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com> wrote:
> >>
> >> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> >>> simply amber ff for small molecules.
> >>> You have to get first amber tools. The last release is amber tools 16
> >>> Get the source code from here :
> >>> http://ambermd.org/AmberTools16-get.html
> >>>
> >>> after installation you can use antechamber for creating the
> >>> small-molecule
> >>> parameters
> >>>
> >>> later, you can use a nice free program called ACEPYP, made to convert
> >>> amber
> >>> parameters to gromacs toplogyget the code from here:
> >>>
> >>> https://github.com/t-/acpype
> >>>
> >>> Regards
> >>>
> >>>
> >>>
> >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> >>> za.par...@gmail.com> wrote:
> >>>
> >>> Dear Sir
> >>>>
> >>>> Thank you very much for your reply. Can you give me any link or
> >>>>
> >>> suggestion
> >>>
> >>>> that i can learn for amber force field for protein and ligand.
> >>>>
> >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu>
> wrote:
> >>>>
> >>>>
> >>>>>
> >>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> >>>>>
> >>>>> Dear Sir
> >>>>>>
> >>>>>> I am new for protein-ligand complex. I want amber force field (ff03)
> >>>>>>
> >>>>> for
> >>>
> >>>> my
> >>>>>> protein, tip3p for water model and gaff (General Amber force field)
> >>>>>>
> >>>>> for
> >>>
> >>>> ligand. I do not know how to produce gaff force field from pdb and
> >>>>>>
> >>>>> then
> >>>
> >>>> convert for gromacs topology.
> >>>>>>
> >>>>>> I have tried ff03 with gromos ligand topology and tip3p water model
> >>>>>>
> >>>>>> it gives me the error:
> >>>>>> atomtype OM not found
> >>>>>>
> >>>>>> and when I have tried ff03 with gromos topology and spc water model
> it
> >>>>>> gives me the error like:
> >>>>>> atomtype HW not found.
> >>>>>>
> >>>>>> Can anyone help me about it?
> >>&g

Re: [gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

I have just use acpype.py -i OAI.pdb
I am getting the error:
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting !
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
What 'which antechamber' in your terminal says?
'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second

I am thinking that I have to install amber. But I dont want to do that. Is
there any way that I can create ligand topology for gaff.



On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
>
>> Ok, you should not mix and match forcefields, ¿but in the case of
>> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
>>
>
> GAFF is compatible with AMBER (by design).  My comments were warning that
> one should not use AMBER for a protein in concert with GROMOS for a ligand.
>
> -Justin
>
> Best regards.
>> Lucio Montero.
>>
>> Enviado desde Correo para Windows 10
>>
>> De: Alan
>> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
>> Para: Gromacs
>> Asunto: Re: [gmx-users] ligand topology
>>
>> Please this GitHub link is totally outdated and not linked in any sense to
>> the original authors.
>>
>> Get the correct ACPYPE here:
>>
>> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
>> stable/ccpn/python/acpype acpype
>>
>> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com> wrote:
>>
>> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
>>> simply amber ff for small molecules.
>>> You have to get first amber tools. The last release is amber tools 16
>>> Get the source code from here :
>>> http://ambermd.org/AmberTools16-get.html
>>>
>>> after installation you can use antechamber for creating the
>>> small-molecule
>>> parameters
>>>
>>> later, you can use a nice free program called ACEPYP, made to convert
>>> amber
>>> parameters to gromacs toplogyget the code from here:
>>>
>>> https://github.com/t-/acpype
>>>
>>> Regards
>>>
>>>
>>>
>>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
>>> za.par...@gmail.com> wrote:
>>>
>>> Dear Sir
>>>>
>>>> Thank you very much for your reply. Can you give me any link or
>>>>
>>> suggestion
>>>
>>>> that i can learn for amber force field for protein and ligand.
>>>>
>>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>
>>>>
>>>>>
>>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
>>>>>
>>>>> Dear Sir
>>>>>>
>>>>>> I am new for protein-ligand complex. I want amber force field (ff03)
>>>>>>
>>>>> for
>>>
>>>> my
>>>>>> protein, tip3p for water model and gaff (General Amber force field)
>>>>>>
>>>>> for
>>>
>>>> ligand. I do not know how to produce gaff force field from pdb and
>>>>>>
>>>>> then
>>>
>>>> convert for gromacs topology.
>>>>>>
>>>>>> I have tried ff03 with gromos ligand topology and tip3p water model
>>>>>>
>>>>>> it gives me the error:
>>>>>> atomtype OM not found
>>>>>>
>>>>>> and when I have tried ff03 with gromos topology and spc water model it
>>>>>> gives me the error like:
>>>>>> atomtype HW not found.
>>>>>>
>>>>>> Can anyone help me about it?
>>>>>>
>>>>>>
>>>>>> You can't mix and match force fields; it's fundamentally wrong.  You
>>>>>
>>>> need
>>>
>>>> to develop ligand parameters that are consistent with the parent
>>>>>
>>>> protein
>>>
>>>> force field.  Various tools exist for different force fields, with
>>>>>
>>>> varying
>>>>
>>>>> degrees of reliability.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==
>>>>>
>>>>> Just

Re: [gmx-users] ligand topology

[Justin Lemkul]

On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:

Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for 
the protein and gaff for ligand? (TIP3P wáter).


GAFF is compatible with AMBER (by design).  My comments were warning that one 
should not use AMBER for a protein in concert with GROMOS for a ligand.


-Justin


Best regards.
Lucio Montero.

Enviado desde Correo para Windows 10

De: Alan
Enviado: martes, 1 de agosto de 2017 11:01 a. m.
Para: Gromacs
Asunto: Re: [gmx-users] ligand topology

Please this GitHub link is totally outdated and not linked in any sense to
the original authors.

Get the correct ACPYPE here:

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com> wrote:


Actually, GAFF forcefield and amber forcefields are compatible. gaff is
simply amber ff for small molecules.
You have to get first amber tools. The last release is amber tools 16
Get the source code from here :
http://ambermd.org/AmberTools16-get.html

after installation you can use antechamber for creating the small-molecule
parameters

later, you can use a nice free program called ACEPYP, made to convert amber
parameters to gromacs toplogyget the code from here:

https://github.com/t-/acpype

Regards



On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
za.par...@gmail.com> wrote:


Dear Sir

Thank you very much for your reply. Can you give me any link or

suggestion

that i can learn for amber force field for protein and ligand.

On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:




On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:


Dear Sir

I am new for protein-ligand complex. I want amber force field (ff03)

for

my
protein, tip3p for water model and gaff (General Amber force field)

for

ligand. I do not know how to produce gaff force field from pdb and

then

convert for gromacs topology.

I have tried ff03 with gromos ligand topology and tip3p water model

it gives me the error:
atomtype OM not found

and when I have tried ff03 with gromos topology and spc water model it
gives me the error like:
atomtype HW not found.

Can anyone help me about it?



You can't mix and match force fields; it's fundamentally wrong.  You

need

to develop ligand parameters that are consistent with the parent

protein

force field.  Various tools exist for different force fields, with

varying

degrees of reliability.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

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send a mail to gmx-users-requ...@gromacs.org.





--


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*
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Support/Mailing_Lists/GMX-Users_List before posting!

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send a mail to gmx-users-requ...@gromacs.org.





--
Dr. rer. nat. Suhaib Shekfeh
PhD in Computational Drug Design and Medicinal Chemistry
Oleariusstr. 11, Halle (Saale), Germany
LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
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send a mail to gmx-users-requ...@gromacs.org.







--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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* Please search the archive at 
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Re: [gmx-users] ligand topology

[Lucio Ricardo Montero Valenzuela]

Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for 
the protein and gaff for ligand? (TIP3P wáter).
Best regards.
Lucio Montero.

Enviado desde Correo para Windows 10

De: Alan
Enviado: martes, 1 de agosto de 2017 11:01 a. m.
Para: Gromacs
Asunto: Re: [gmx-users] ligand topology

Please this GitHub link is totally outdated and not linked in any sense to
the original authors.

Get the correct ACPYPE here:

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com> wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@grom

Re: [gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

Thank you very much.

On Tue, Aug 1, 2017 at 7:00 AM, Suhaib Shekfeh  wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu *
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Dr. rer. nat. Suhaib Shekfeh
> PhD in Computational Drug Design and Medicinal Chemistry
> Oleariusstr. 11, Halle (Saale), Germany
> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ligand topology

[Alan]

Please this GitHub link is totally outdated and not linked in any sense to
the original authors.

Get the correct ACPYPE here:

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

On 1 August 2017 at 15:00, Suhaib Shekfeh  wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu *
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Dr. rer. nat. Suhaib Shekfeh
> PhD in Computational Drug Design and Medicinal Chemistry
> Oleariusstr. 11, Halle (Saale), Germany
> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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mail to 

Re: [gmx-users] ligand topology

[Suhaib Shekfeh]

Actually, GAFF forcefield and amber forcefields are compatible. gaff is
simply amber ff for small molecules.
You have to get first amber tools. The last release is amber tools 16
Get the source code from here :
http://ambermd.org/AmberTools16-get.html

after installation you can use antechamber for creating the small-molecule
parameters

later, you can use a nice free program called ACEPYP, made to convert amber
parameters to gromacs toplogyget the code from here:

https://github.com/t-/acpype

Regards



On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
za.par...@gmail.com> wrote:

> Dear Sir
>
> Thank you very much for your reply. Can you give me any link or suggestion
> that i can learn for amber force field for protein and ligand.
>
> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> >
> >> Dear Sir
> >>
> >> I am new for protein-ligand complex. I want amber force field (ff03) for
> >> my
> >> protein, tip3p for water model and gaff (General Amber force field) for
> >> ligand. I do not know how to produce gaff force field from pdb and then
> >> convert for gromacs topology.
> >>
> >> I have tried ff03 with gromos ligand topology and tip3p water model
> >>
> >> it gives me the error:
> >> atomtype OM not found
> >>
> >> and when I have tried ff03 with gromos topology and spc water model it
> >> gives me the error like:
> >> atomtype HW not found.
> >>
> >> Can anyone help me about it?
> >>
> >>
> > You can't mix and match force fields; it's fundamentally wrong.  You need
> > to develop ligand parameters that are consistent with the parent protein
> > force field.  Various tools exist for different force fields, with
> varying
> > degrees of reliability.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
>
>
> *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> *Email: khan5...@vandals.uidaho.edu *
> * Skype: parash.khan2*
> *Cell: +12085967165*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Dr. rer. nat. Suhaib Shekfeh
PhD in Computational Drug Design and Medicinal Chemistry
Oleariusstr. 11, Halle (Saale), Germany
LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

Thank you very much for your reply. Can you give me any link or suggestion
that i can learn for amber force field for protein and ligand.

On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:

>
>
> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> Dear Sir
>>
>> I am new for protein-ligand complex. I want amber force field (ff03) for
>> my
>> protein, tip3p for water model and gaff (General Amber force field) for
>> ligand. I do not know how to produce gaff force field from pdb and then
>> convert for gromacs topology.
>>
>> I have tried ff03 with gromos ligand topology and tip3p water model
>>
>> it gives me the error:
>> atomtype OM not found
>>
>> and when I have tried ff03 with gromos topology and spc water model it
>> gives me the error like:
>> atomtype HW not found.
>>
>> Can anyone help me about it?
>>
>>
> You can't mix and match force fields; it's fundamentally wrong.  You need
> to develop ligand parameters that are consistent with the parent protein
> force field.  Various tools exist for different force fields, with varying
> degrees of reliability.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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[gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

I am new for protein-ligand complex. I want amber force field (ff03) for my
protein, tip3p for water model and gaff (General Amber force field) for
ligand. I do not know how to produce gaff force field from pdb and then
convert for gromacs topology.

I have tried ff03 with gromos ligand topology and tip3p water model

it gives me the error:
atomtype OM not found

and when I have tried ff03 with gromos topology and spc water model it
gives me the error like:
atomtype HW not found.

Can anyone help me about it?

-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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[gmx-users] Ligand topology

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Dear gromacs users
Is there any way to create ligand topology file by using pdb2gmx instead of 
prodrg? Because i use gromos 43a1 ff for making protein topology and use prodrg 
to create ligand topoligy and .gro file. But i dont know anything about 
reparametrizing the ligand topology but reassigning charge and charge groups. 
Is there anyone can help me:1) is it possible to make ligand topology file by 
pdb2gmx 2) what kind of reparametrizations are needed to be done to obtain the 
proper ligand topol.top file but reassigning charges and charge groups that 

Sent from Yahoo Mail for iPhone
 
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Re: [gmx-users] Ligand and ion topology

[Justin Lemkul]

On 7/4/17 5:33 AM, Khadija Amine wrote:

Dear gromacs users,

I have a protein with GNP ligand and acetate ACT ion that I want to
simulate.

I have prepared topologies for both GNP and ACT with PRODRG program.



Don't use PRODRG unless you manually reparametrize the charges and charge groups 
afterward.



My first question is: Where should I exactly include the ACT.itp and
GNP.itp into topol.top file?



In principle, anywhere after the initial force field #include statement, as long 
as no new parameter types are introduced.



My second question is:
I have Copied and pasted the coordinates from my two molecules files onto
the end of the protein.gro file. I have changed the number at the top or
beginning of the file from as it should be to corrected the total number of
atoms in the file.

Should I change the atom number column and renumber the atoms with the new
ones?



mdrun doesn't care about coordinate file numbering.


Is this will affect the position of the ligand and the ions in the protein
structure?



Only coordinates affect positions, not atom numbers.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Ligand and ion topology

[Khadija Amine]

Can anyone help, please?



*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
Phone: 9584

On Tue, Jul 4, 2017 at 12:33 PM, Khadija Amine  wrote:

> Dear gromacs users,
>
> I have a protein with GNP ligand and acetate ACT ion that I want to
> simulate.
>
> I have prepared topologies for both GNP and ACT with PRODRG program.
>
> My first question is: Where should I exactly include the ACT.itp and
> GNP.itp into topol.top file?
>
> My second question is:
> I have Copied and pasted the coordinates from my two molecules files onto
> the end of the protein.gro file. I have changed the number at the top or
> beginning of the file from as it should be to corrected the total number of
> atoms in the file.
>
> Should I change the atom number column and renumber the atoms with the new
> ones?
>
> Is this will affect the position of the ligand and the ions in the protein
> structure?
>
> Thank you
>
> *Khadija Amine*
> Ph.D. Biology and Health
> Biochemistry & Bioinformatics
> Phone: 9584
>
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[gmx-users] Ligand and ion topology

[Khadija Amine]

Dear gromacs users,

I have a protein with GNP ligand and acetate ACT ion that I want to
simulate.

I have prepared topologies for both GNP and ACT with PRODRG program.

My first question is: Where should I exactly include the ACT.itp and
GNP.itp into topol.top file?

My second question is:
I have Copied and pasted the coordinates from my two molecules files onto
the end of the protein.gro file. I have changed the number at the top or
beginning of the file from as it should be to corrected the total number of
atoms in the file.

Should I change the atom number column and renumber the atoms with the new
ones?

Is this will affect the position of the ligand and the ions in the protein
structure?

Thank you

*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
Phone: 9584
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/22/17 4:04 AM, abhisek Mondal wrote:

I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) and applied as pull-coord1-vec.
However, I hate to say, after 500-600ps md_umbrella run the ligand got out
of the active site again. It is becoming very painful.
As you asked lastly, due to flexible ligand scenario. I'm further thinking
not to use ligand COM, despite coordinate of some atoms near the ring
structure. However, I'm totally confused regarding whether this approach
will work out. Giving it a try though.



If your ligand is large and flexible or the protein rotates very quickly, then 
it will be hard to define the reaction coordinate in the manner that we've been 
trying.  You may have to move to something more generic like distance geometry 
with pull_dim = Y Y Y and a very large box (obviously computationally expensive) 
or you'll have to calculate the binding free energy another way entirely 
(alchemical transformation, MM/PBSA, etc).


-Justin




On Sun, May 21, 2017 at 8:39 PM, abhisek Mondal 
wrote:


Beg your pardon, I have not ignored your comment entirely regarding using
specific residue COM. I just recently succeeded performing md_umbrella
simulation (using protein COM) on few configurations.
.
I have not used specific residues COM so far as because of some confusions
regrading defining it. The residue stretch is not continuous e.g. residue
6-10, 78-80, 56, 63, 35 are to be active site residue. I got no idea how to
define such discrete set of residues using make_ndx command.



On Sun, May 21, 2017 at 8:13 PM, Justin Lemkul  wrote:




On 5/21/17 9:47 AM, abhisek Mondal wrote:


I did try the code successfully on a configuration generated after
pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.

However, when I tried to reapply the same code (with modified COMs and
thus
pull_vec) on a different configuration, something awkward happened. The
ligand got pulled through protein and got stuck inside it. I have put the
trajectory movie alongwith md_umbrella.mdp file here:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Would you please care to give some advise regarding this odd behavior.



Likely some elements of your setup are inadequate.  You have a large,
flexible ligand, so perhaps using its overall COM is inappropriate.  You're
also using the entire protein COM as the other end of the reaction
coordinate, and perhaps that's not good enough (I've suggested a number of
times to be judicious in the choice of residues taken as the group
corresponding to the protein, but it seems you're simply not doing that so
I'll stop suggesting it).  Perhaps your pull vector is calculated
incorrectly.  A lot going on.  Back up and do something simpler, a test
case that is easy to define so you can get comfortable with setting these
things up and understanding/diagnosing weird behavior.

-Justin


Thank you.


On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:




On 5/19/17 5:56 AM, abhisek Mondal wrote:

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:





On 5/17/17 8:55 AM, abhisek Mondal wrote:

This time I think I got ligand restrained successfully during the


umbrella
sampling. I have removed the restrain from protein, as per your
advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and
used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the
following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving
around
the
box and resulting in "Distance of pull group 1 (10.441990 nm) is
larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked,
then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have
taken
pretty large box compared to the protein structure from the
beginning.

Please suggest me a way out.


Use a larger box or use direction-periodic geometry.






 For the sake of computational power I'm leaning towards
direction-periodic
geometry. However, from the mailing list entries I found out that
pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There
are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
looks
sensible ?

Eagerly waiting for your opinion.


Try it and see what happens.

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) and applied as pull-coord1-vec.
However, I hate to say, after 500-600ps md_umbrella run the ligand got out
of the active site again. It is becoming very painful.
As you asked lastly, due to flexible ligand scenario. I'm further thinking
not to use ligand COM, despite coordinate of some atoms near the ring
structure. However, I'm totally confused regarding whether this approach
will work out. Giving it a try though.



On Sun, May 21, 2017 at 8:39 PM, abhisek Mondal 
wrote:

> Beg your pardon, I have not ignored your comment entirely regarding using
> specific residue COM. I just recently succeeded performing md_umbrella
> simulation (using protein COM) on few configurations.
> .
> I have not used specific residues COM so far as because of some confusions
> regrading defining it. The residue stretch is not continuous e.g. residue
> 6-10, 78-80, 56, 63, 35 are to be active site residue. I got no idea how to
> define such discrete set of residues using make_ndx command.
>
>
>
> On Sun, May 21, 2017 at 8:13 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/21/17 9:47 AM, abhisek Mondal wrote:
>>
>>> I did try the code successfully on a configuration generated after
>>> pulling.
>>> The NVT approach with direction-periodic geometry worked nicely for the
>>> particular configuration.
>>>
>>> However, when I tried to reapply the same code (with modified COMs and
>>> thus
>>> pull_vec) on a different configuration, something awkward happened. The
>>> ligand got pulled through protein and got stuck inside it. I have put the
>>> trajectory movie alongwith md_umbrella.mdp file here:
>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>>
>>> Would you please care to give some advise regarding this odd behavior.
>>>
>>>
>> Likely some elements of your setup are inadequate.  You have a large,
>> flexible ligand, so perhaps using its overall COM is inappropriate.  You're
>> also using the entire protein COM as the other end of the reaction
>> coordinate, and perhaps that's not good enough (I've suggested a number of
>> times to be judicious in the choice of residues taken as the group
>> corresponding to the protein, but it seems you're simply not doing that so
>> I'll stop suggesting it).  Perhaps your pull vector is calculated
>> incorrectly.  A lot going on.  Back up and do something simpler, a test
>> case that is easy to define so you can get comfortable with setting these
>> things up and understanding/diagnosing weird behavior.
>>
>> -Justin
>>
>>
>> Thank you.
>>>
>>> On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:
>>>
>>>

 On 5/19/17 5:56 AM, abhisek Mondal wrote:

 On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:
>
>
>
>> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>>
>> This time I think I got ligand restrained successfully during the
>>
>>> umbrella
>>> sampling. I have removed the restrain from protein, as per your
>>> advice.
>>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and
>>> used
>>> pull_rate1=0.0.
>>> I have uploaded the trajectory movie (and other mdp files) in the
>>> following
>>> link:
>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>>
>>> However, I'm facing a problem. Due to the withdrawal of the position
>>> restrain of protein. The protein and ligand (together) is moving
>>> around
>>> the
>>> box and resulting in "Distance of pull group 1 (10.441990 nm) is
>>> larger
>>> than 0.49 times the box size (10.646989)" error.
>>>
>>> As per the video I have uploaded, if I assume this approach worked,
>>> then
>>> how can I avoid this error ? Is  there any way to make sure the
>>> protein-ligand remains in the middle of the box (or nearby). I have
>>> taken
>>> pretty large box compared to the protein structure from the
>>> beginning.
>>>
>>> Please suggest me a way out.
>>>
>>>
>>> Use a larger box or use direction-periodic geometry.
>>>
>>
>>
>
>  For the sake of computational power I'm leaning towards
> direction-periodic
> geometry. However, from the mailing list entries I found out that
> pressure
> coupling should not be used for this kind of geometry setup.
> NVT coupling with no velocity generation is what I'm opting for. There
> are
> a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
> Would you please suggest if the code (
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
> looks
> sensible ?
>
> Eagerly waiting for your 

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Beg your pardon, I have not ignored your comment entirely regarding using
specific residue COM. I just recently succeeded performing md_umbrella
simulation (using protein COM) on few configurations.
.
I have not used specific residues COM so far as because of some confusions
regrading defining it. The residue stretch is not continuous e.g. residue
6-10, 78-80, 56, 63, 35 are to be active site residue. I got no idea how to
define such discrete set of residues using make_ndx command.



On Sun, May 21, 2017 at 8:13 PM, Justin Lemkul  wrote:

>
>
> On 5/21/17 9:47 AM, abhisek Mondal wrote:
>
>> I did try the code successfully on a configuration generated after
>> pulling.
>> The NVT approach with direction-periodic geometry worked nicely for the
>> particular configuration.
>>
>> However, when I tried to reapply the same code (with modified COMs and
>> thus
>> pull_vec) on a different configuration, something awkward happened. The
>> ligand got pulled through protein and got stuck inside it. I have put the
>> trajectory movie alongwith md_umbrella.mdp file here:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>> Would you please care to give some advise regarding this odd behavior.
>>
>>
> Likely some elements of your setup are inadequate.  You have a large,
> flexible ligand, so perhaps using its overall COM is inappropriate.  You're
> also using the entire protein COM as the other end of the reaction
> coordinate, and perhaps that's not good enough (I've suggested a number of
> times to be judicious in the choice of residues taken as the group
> corresponding to the protein, but it seems you're simply not doing that so
> I'll stop suggesting it).  Perhaps your pull vector is calculated
> incorrectly.  A lot going on.  Back up and do something simpler, a test
> case that is easy to define so you can get comfortable with setting these
> things up and understanding/diagnosing weird behavior.
>
> -Justin
>
>
> Thank you.
>>
>> On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/19/17 5:56 AM, abhisek Mondal wrote:
>>>
>>> On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:



> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>
> This time I think I got ligand restrained successfully during the
>
>> umbrella
>> sampling. I have removed the restrain from protein, as per your
>> advice.
>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and
>> used
>> pull_rate1=0.0.
>> I have uploaded the trajectory movie (and other mdp files) in the
>> following
>> link:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>> However, I'm facing a problem. Due to the withdrawal of the position
>> restrain of protein. The protein and ligand (together) is moving
>> around
>> the
>> box and resulting in "Distance of pull group 1 (10.441990 nm) is
>> larger
>> than 0.49 times the box size (10.646989)" error.
>>
>> As per the video I have uploaded, if I assume this approach worked,
>> then
>> how can I avoid this error ? Is  there any way to make sure the
>> protein-ligand remains in the middle of the box (or nearby). I have
>> taken
>> pretty large box compared to the protein structure from the beginning.
>>
>> Please suggest me a way out.
>>
>>
>> Use a larger box or use direction-periodic geometry.
>>
>
>

  For the sake of computational power I'm leaning towards
 direction-periodic
 geometry. However, from the mailing list entries I found out that
 pressure
 coupling should not be used for this kind of geometry setup.
 NVT coupling with no velocity generation is what I'm opting for. There
 are
 a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
 Would you please suggest if the code (
 https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
 looks
 sensible ?

 Eagerly waiting for your opinion.


 Try it and see what happens.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> 

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/21/17 9:47 AM, abhisek Mondal wrote:

I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.

However, when I tried to reapply the same code (with modified COMs and thus
pull_vec) on a different configuration, something awkward happened. The
ligand got pulled through protein and got stuck inside it. I have put the
trajectory movie alongwith md_umbrella.mdp file here:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Would you please care to give some advise regarding this odd behavior.



Likely some elements of your setup are inadequate.  You have a large, flexible 
ligand, so perhaps using its overall COM is inappropriate.  You're also using 
the entire protein COM as the other end of the reaction coordinate, and perhaps 
that's not good enough (I've suggested a number of times to be judicious in the 
choice of residues taken as the group corresponding to the protein, but it seems 
you're simply not doing that so I'll stop suggesting it).  Perhaps your pull 
vector is calculated incorrectly.  A lot going on.  Back up and do something 
simpler, a test case that is easy to define so you can get comfortable with 
setting these things up and understanding/diagnosing weird behavior.


-Justin


Thank you.

On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:




On 5/19/17 5:56 AM, abhisek Mondal wrote:


On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:




On 5/17/17 8:55 AM, abhisek Mondal wrote:

This time I think I got ligand restrained successfully during the

umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the
following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving around
the
box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked, then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have
taken
pretty large box compared to the protein structure from the beginning.

Please suggest me a way out.


Use a larger box or use direction-periodic geometry.





 For the sake of computational power I'm leaning towards
direction-periodic
geometry. However, from the mailing list entries I found out that pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
looks
sensible ?

Eagerly waiting for your opinion.



Try it and see what happens.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.

However, when I tried to reapply the same code (with modified COMs and thus
pull_vec) on a different configuration, something awkward happened. The
ligand got pulled through protein and got stuck inside it. I have put the
trajectory movie alongwith md_umbrella.mdp file here:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Would you please care to give some advise regarding this odd behavior.

Thank you.

On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:

>
>
> On 5/19/17 5:56 AM, abhisek Mondal wrote:
>
>> On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>>>
>>> This time I think I got ligand restrained successfully during the
 umbrella
 sampling. I have removed the restrain from protein, as per your advice.
 Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
 pull_rate1=0.0.
 I have uploaded the trajectory movie (and other mdp files) in the
 following
 link:
 https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

 However, I'm facing a problem. Due to the withdrawal of the position
 restrain of protein. The protein and ligand (together) is moving around
 the
 box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
 than 0.49 times the box size (10.646989)" error.

 As per the video I have uploaded, if I assume this approach worked, then
 how can I avoid this error ? Is  there any way to make sure the
 protein-ligand remains in the middle of the box (or nearby). I have
 taken
 pretty large box compared to the protein structure from the beginning.

 Please suggest me a way out.


 Use a larger box or use direction-periodic geometry.
>>>
>>
>>
>>  For the sake of computational power I'm leaning towards
>> direction-periodic
>> geometry. However, from the mailing list entries I found out that pressure
>> coupling should not be used for this kind of geometry setup.
>> NVT coupling with no velocity generation is what I'm opting for. There are
>> a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
>> Would you please suggest if the code (
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
>> looks
>> sensible ?
>>
>> Eagerly waiting for your opinion.
>>
>>
> Try it and see what happens.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
Gromacs Users mailing list

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/19/17 5:56 AM, abhisek Mondal wrote:

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:




On 5/17/17 8:55 AM, abhisek Mondal wrote:


This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the
following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving around
the
box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked, then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have taken
pretty large box compared to the protein structure from the beginning.

Please suggest me a way out.



Use a larger box or use direction-periodic geometry.



 For the sake of computational power I'm leaning towards direction-periodic
geometry. However, from the mailing list entries I found out that pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0) looks
sensible ?

Eagerly waiting for your opinion.



Try it and see what happens.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:

>
>
> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>
>> This time I think I got ligand restrained successfully during the umbrella
>> sampling. I have removed the restrain from protein, as per your advice.
>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
>> pull_rate1=0.0.
>> I have uploaded the trajectory movie (and other mdp files) in the
>> following
>> link:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>> However, I'm facing a problem. Due to the withdrawal of the position
>> restrain of protein. The protein and ligand (together) is moving around
>> the
>> box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
>> than 0.49 times the box size (10.646989)" error.
>>
>> As per the video I have uploaded, if I assume this approach worked, then
>> how can I avoid this error ? Is  there any way to make sure the
>> protein-ligand remains in the middle of the box (or nearby). I have taken
>> pretty large box compared to the protein structure from the beginning.
>>
>> Please suggest me a way out.
>>
>>
> Use a larger box or use direction-periodic geometry.


 For the sake of computational power I'm leaning towards direction-periodic
geometry. However, from the mailing list entries I found out that pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0) looks
sensible ?

Eagerly waiting for your opinion.



>
> -Justin
>
>
> On Mon, May 15, 2017 at 5:48 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/15/17 2:45 AM, abhisek Mondal wrote:
>>>
>>> On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:



> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <
> abhisek.m...@gmail.com
>
>>
>>> wrote:
>>
>> Hi,
>>
>>
>>> Thank you for the explanation. It really cleared some concepts. But
>>> I'm
>>> still having my ligand moving in this step. I have modified the code
>>> as:
>>> ; Pull code
>>> pull= umbrella
>>> pull_ngroups= 1
>>> pull_group0 = Protein_chain_A
>>> pull_group1 = ACO
>>> pull_geometry   = direction ; simple distance increase
>>> pull_dim   = Y Y Y ; not to allow ligand move along
>>> other
>>> dir
>>> pull_rate1 = 0.0
>>> pull_k1   = 1000   ; kJ mol^-1 nm^-2
>>> pull_start   = yes   ; define initial COM distance > 0
>>> pull_vec1   = 0 0 -1
>>>
>>>
>>> Note that with "direction" geometry, only pull_vec1 is acting.
>>>
>> pull_dim
> is ignored.
>
> The ligand was previously moving along x,y direction when I was using
>
> pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
>>
>>> as
>>> vector  and pull_rate1=0.0, so that it does not move much. But at the
>>> end
>>> of a 10ns run, I see that the ligand is still moving as it was
>>> earlier.
>>>
>>> It shows me:
>>>
>>>  Pull group  natoms  pbc atom  distance at start reference at t=0
>>0  1132936665
>>159  1618  -1.555-1.555
>> Is it ok withe negative value ? Anyway this setup is not working.
>>
>>
>> Again you're trying to just apply the restraint to one dimension and
>> it
>>
> looks to be fairly arbitrary.  I already suggested using the vector
> connecting the ligand COM with the binding site residues' COM and using
> that as pull_vec1.  Draw it out.  It makes a lot more sense than trying
> to
> restrain only along one axis, which as I have said before, makes no
> sense
> in this case.
>
> Thank you for such detailed suggestion.
>
> I followed on as per your suggestion. Calculated COM of protein and
 Ligand.
 Calculated protein-lig vector (using COM) to be used for pulling (as
 pull_vec1).
 Pulling also achieved successfully.
 But after pulling, when I performed the brief npt_umbrella run with
 pull_rate1=0, I found the ligand is moving little bit. Could not
 understand
 what I have mistaken this time.
 So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and
 pull_vec1=as determined from COM calculations. Despite I found that the
 ligand is moving vigorously and got pulled away probably.
 I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for
 npt_umbrella), npt140.gro,md_umbrella run video in the following link:
 

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/17/17 8:55 AM, abhisek Mondal wrote:

This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving around the
box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked, then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have taken
pretty large box compared to the protein structure from the beginning.

Please suggest me a way out.



Use a larger box or use direction-periodic geometry.

-Justin


On Mon, May 15, 2017 at 5:48 PM, Justin Lemkul  wrote:




On 5/15/17 2:45 AM, abhisek Mondal wrote:


On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:




On 5/11/17 9:21 AM, abhisek Mondal wrote:

On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal  0
pull_vec1   = 0 0 -1


Note that with "direction" geometry, only pull_vec1 is acting.

pull_dim
is ignored.

The ligand was previously moving along x,y direction when I was using


pull_dim  = N N Y. So I changed it to Y in all direction and provided 0

as
vector  and pull_rate1=0.0, so that it does not move much. But at the
end
of a 10ns run, I see that the ligand is still moving as it was earlier.

It shows me:


 Pull group  natoms  pbc atom  distance at start reference at t=0
   0  1132936665
   159  1618  -1.555-1.555
Is it ok withe negative value ? Anyway this setup is not working.


Again you're trying to just apply the restraint to one dimension and it

looks to be fairly arbitrary.  I already suggested using the vector
connecting the ligand COM with the binding site residues' COM and using
that as pull_vec1.  Draw it out.  It makes a lot more sense than trying
to
restrain only along one axis, which as I have said before, makes no sense
in this case.

Thank you for such detailed suggestion.


I followed on as per your suggestion. Calculated COM of protein and
Ligand.
Calculated protein-lig vector (using COM) to be used for pulling (as
pull_vec1).
Pulling also achieved successfully.
But after pulling, when I performed the brief npt_umbrella run with
pull_rate1=0, I found the ligand is moving little bit. Could not
understand
what I have mistaken this time.
So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and
pull_vec1=as determined from COM calculations. Despite I found that the
ligand is moving vigorously and got pulled away probably.
I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for
npt_umbrella), npt140.gro,md_umbrella run video in the following link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0


Am I still missing some drastic steps ? Please suggest me if I do. I'm
totally lost here in this regard.



Again, don't restrain the protein.  I've said this multiple times.

The pull setup looks reasonable.  Maybe you just need a stronger force
constant, or you should not use the COM of the whole protein, instead the
COM of a few important residues (use an index group with gmx traj -ox -com
to get its coordinates).  If the specified vector is off, so too will be
the resulting biasing potential.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For 

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

This time I think I got ligand restrained successfully during the umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving around the
box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked, then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have taken
pretty large box compared to the protein structure from the beginning.

Please suggest me a way out.

On Mon, May 15, 2017 at 5:48 PM, Justin Lemkul  wrote:

>
>
> On 5/15/17 2:45 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>>>
>>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
 wrote:

 Hi,

>
> Thank you for the explanation. It really cleared some concepts. But I'm
> still having my ligand moving in this step. I have modified the code
> as:
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = Protein_chain_A
> pull_group1 = ACO
> pull_geometry   = direction ; simple distance increase
> pull_dim   = Y Y Y ; not to allow ligand move along
> other
> dir
> pull_rate1 = 0.0
> pull_k1   = 1000   ; kJ mol^-1 nm^-2
> pull_start   = yes   ; define initial COM distance > 0
> pull_vec1   = 0 0 -1
>
>
> Note that with "direction" geometry, only pull_vec1 is acting.
>>> pull_dim
>>> is ignored.
>>>
>>> The ligand was previously moving along x,y direction when I was using
>>>
 pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
> as
> vector  and pull_rate1=0.0, so that it does not move much. But at the
> end
> of a 10ns run, I see that the ligand is still moving as it was earlier.
>
> It shows me:
>
  Pull group  natoms  pbc atom  distance at start reference at t=0
0  1132936665
159  1618  -1.555-1.555
 Is it ok withe negative value ? Anyway this setup is not working.


 Again you're trying to just apply the restraint to one dimension and it
>>> looks to be fairly arbitrary.  I already suggested using the vector
>>> connecting the ligand COM with the binding site residues' COM and using
>>> that as pull_vec1.  Draw it out.  It makes a lot more sense than trying
>>> to
>>> restrain only along one axis, which as I have said before, makes no sense
>>> in this case.
>>>
>>> Thank you for such detailed suggestion.
>>>
>> I followed on as per your suggestion. Calculated COM of protein and
>> Ligand.
>> Calculated protein-lig vector (using COM) to be used for pulling (as
>> pull_vec1).
>> Pulling also achieved successfully.
>> But after pulling, when I performed the brief npt_umbrella run with
>> pull_rate1=0, I found the ligand is moving little bit. Could not
>> understand
>> what I have mistaken this time.
>> So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and
>> pull_vec1=as determined from COM calculations. Despite I found that the
>> ligand is moving vigorously and got pulled away probably.
>> I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for
>> npt_umbrella), npt140.gro,md_umbrella run video in the following link:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>>
>> Am I still missing some drastic steps ? Please suggest me if I do. I'm
>> totally lost here in this regard.
>>
>>
> Again, don't restrain the protein.  I've said this multiple times.
>
> The pull setup looks reasonable.  Maybe you just need a stronger force
> constant, or you should not use the COM of the whole protein, instead the
> COM of a few important residues (use an index group with gmx traj -ox -com
> to get its coordinates).  If the specified vector is off, so too will be
> the resulting biasing potential.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> 

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/15/17 2:45 AM, abhisek Mondal wrote:

On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:




On 5/11/17 9:21 AM, abhisek Mondal wrote:


On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
wrote:

Hi,


Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry   = direction ; simple distance increase
pull_dim   = Y Y Y ; not to allow ligand move along other
dir
pull_rate1 = 0.0
pull_k1   = 1000   ; kJ mol^-1 nm^-2
pull_start   = yes   ; define initial COM distance > 0
pull_vec1   = 0 0 -1



Note that with "direction" geometry, only pull_vec1 is acting.  pull_dim
is ignored.

The ligand was previously moving along x,y direction when I was using

pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
as
vector  and pull_rate1=0.0, so that it does not move much. But at the end
of a 10ns run, I see that the ligand is still moving as it was earlier.

It shows me:

 Pull group  natoms  pbc atom  distance at start reference at t=0
   0  1132936665
   159  1618  -1.555-1.555
Is it ok withe negative value ? Anyway this setup is not working.



Again you're trying to just apply the restraint to one dimension and it
looks to be fairly arbitrary.  I already suggested using the vector
connecting the ligand COM with the binding site residues' COM and using
that as pull_vec1.  Draw it out.  It makes a lot more sense than trying to
restrain only along one axis, which as I have said before, makes no sense
in this case.

Thank you for such detailed suggestion.

I followed on as per your suggestion. Calculated COM of protein and Ligand.
Calculated protein-lig vector (using COM) to be used for pulling (as
pull_vec1).
Pulling also achieved successfully.
But after pulling, when I performed the brief npt_umbrella run with
pull_rate1=0, I found the ligand is moving little bit. Could not understand
what I have mistaken this time.
So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and
pull_vec1=as determined from COM calculations. Despite I found that the
ligand is moving vigorously and got pulled away probably.
I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for
npt_umbrella), npt140.gro,md_umbrella run video in the following link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0


Am I still missing some drastic steps ? Please suggest me if I do. I'm
totally lost here in this regard.



Again, don't restrain the protein.  I've said this multiple times.

The pull setup looks reasonable.  Maybe you just need a stronger force constant, 
or you should not use the COM of the whole protein, instead the COM of a few 
important residues (use an index group with gmx traj -ox -com to get its 
coordinates).  If the specified vector is off, so too will be the resulting 
biasing potential.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:

>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in this step. I have modified the code as:
>>> ; Pull code
>>> pull= umbrella
>>> pull_ngroups= 1
>>> pull_group0 = Protein_chain_A
>>> pull_group1 = ACO
>>> pull_geometry   = direction ; simple distance increase
>>> pull_dim   = Y Y Y ; not to allow ligand move along other
>>> dir
>>> pull_rate1 = 0.0
>>> pull_k1   = 1000   ; kJ mol^-1 nm^-2
>>> pull_start   = yes   ; define initial COM distance > 0
>>> pull_vec1   = 0 0 -1
>>>
>>>
> Note that with "direction" geometry, only pull_vec1 is acting.  pull_dim
> is ignored.
>
> The ligand was previously moving along x,y direction when I was using
>>> pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
>>> as
>>> vector  and pull_rate1=0.0, so that it does not move much. But at the end
>>> of a 10ns run, I see that the ligand is still moving as it was earlier.
>>>
>>> It shows me:
>>  Pull group  natoms  pbc atom  distance at start reference at t=0
>>0  1132936665
>>159  1618  -1.555-1.555
>> Is it ok withe negative value ? Anyway this setup is not working.
>>
>>
> Again you're trying to just apply the restraint to one dimension and it
> looks to be fairly arbitrary.  I already suggested using the vector
> connecting the ligand COM with the binding site residues' COM and using
> that as pull_vec1.  Draw it out.  It makes a lot more sense than trying to
> restrain only along one axis, which as I have said before, makes no sense
> in this case.
>
> Thank you for such detailed suggestion.
I followed on as per your suggestion. Calculated COM of protein and Ligand.
Calculated protein-lig vector (using COM) to be used for pulling (as
pull_vec1).
Pulling also achieved successfully.
But after pulling, when I performed the brief npt_umbrella run with
pull_rate1=0, I found the ligand is moving little bit. Could not understand
what I have mistaken this time.
So I moved on for umbrella sampling mdrun step, with pull_rate1=0 and
pull_vec1=as determined from COM calculations. Despite I found that the
ligand is moving vigorously and got pulled away probably.
I'm putting npt_umbrella.mdp,md_umbrella.mdp,conf140.gro(used for
npt_umbrella), npt140.gro,md_umbrella run video in the following link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0


Am I still missing some drastic steps ? Please suggest me if I do. I'm
totally lost here in this regard.





> -Justin
>
>
>>> I have choose my reaction coordinate to be along -Z axis and want to
>>> apply
>>> biasing potential accordingly with restraining the ligand movement. Can
>>> you
>>> please suggest where am I failing with this code ?
>>>
>>> Thank you.
>>>
>>>
>>>
>>> On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul  wrote:
>>>
>>>

 On 5/8/17 10:00 AM, abhisek Mondal wrote:

 On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:
>
>
>
>> On 5/7/17 1:57 AM, abhisek Mondal wrote:
>>
>> Hi,
>>
>>>
>>> For your ease of understanding regarding what is happening during
>>> this
>>> above said umbrella-mdrun, I have shared the trajectory video file
>>> the
>>> following link.
>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>>
>>> Is this normal given that the mdp code being used ? I basically have
>>> no
>>> idea with this step, so please help me out. I'm using gromacs-4.6.2.
>>>
>>>
>>> Your setup is incorrect.  You're applying a biasing potential only
>>>
>> along
>> z, so the ligand can move freely along x and y.  A protein-ligand
>> complex
>> has spherical symmetry, so you should set the reaction coordinate to
>> the
>> vector connecting the ligand with some suitable subset of interacting
>> protein residues.
>>
>>
>
> I don't get it.
> We are trying not to move our configuration (generated after pulling
> simulation) along the reaction coordinate, so for restraining we are
> supposed to set pull_rate1=0.0.
>
>
 Of course.  But you said set pull_k = 0 which does not make sense.  The
 pulling rate *is* zero during umbrella sampling (no net displacement,
 restrain to the specified distance along the reaction coordinate) and
 pulling force constant should be non-zero.

 If applying biasing potential only along z is causing movement along x
 and

> y then what if we apply the biasing potential along x,y,z ? Will it
> cause

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:

>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in this step. I have modified the code as:
>>> ; Pull code
>>> pull= umbrella
>>> pull_ngroups= 1
>>> pull_group0 = Protein_chain_A
>>> pull_group1 = ACO
>>> pull_geometry   = direction ; simple distance increase
>>> pull_dim   = Y Y Y ; not to allow ligand move along other
>>> dir
>>> pull_rate1 = 0.0
>>> pull_k1   = 1000   ; kJ mol^-1 nm^-2
>>> pull_start   = yes   ; define initial COM distance > 0
>>> pull_vec1   = 0 0 -1
>>>
>>>
> Note that with "direction" geometry, only pull_vec1 is acting.  pull_dim
> is ignored.
>
> The ligand was previously moving along x,y direction when I was using
>>> pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
>>> as
>>> vector  and pull_rate1=0.0, so that it does not move much. But at the end
>>> of a 10ns run, I see that the ligand is still moving as it was earlier.
>>>
>>> It shows me:
>>  Pull group  natoms  pbc atom  distance at start reference at t=0
>>0  1132936665
>>159  1618  -1.555-1.555
>> Is it ok withe negative value ? Anyway this setup is not working.
>>
>>
> Again you're trying to just apply the restraint to one dimension and it
> looks to be fairly arbitrary.  I already suggested using the vector
> connecting the ligand COM with the binding site residues' COM and using
> that as pull_vec1.  Draw it out.  It makes a lot more sense than trying to
> restrain only along one axis, which as I have said before, makes no sense
> in this case.


As to obtain COM of ligand I'm using:  "g_traj_mpi -ox aco_com -com -s
npt.tpr" and taking the last frame's xy,z coordinate from the .xvg file
generated from that command.
 394 14.1362 14.4649 5.94131
 395 14.1435 14.45 5.94041
 396 14.0858 14.4461 5.90442
 397 14.1398 14.4164 5.86902
 398 14.1514 14.4434 5.8461
 399 14.1344 14.421 5.88976
 400 14.1996 14.4613 5.82814

Is this approach correct for taking COM?

Another question is that, how can I calculate COM for specific set of
residues ? If the above approach (for calculating Ligand COM) is correct
then it allows calculation of COM for whole protein only.
Please do suggest a way.



Thank you.



>
> -Justin
>
>
>>>
-- 
Gromacs Users mailing list

* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/11/17 1:25 PM, abhisek Mondal wrote:

Alright. I'm trying as per your advice. Actually my system is pretty big
and due to constraint of computation power it is taking me more time to
test vector setup. I really appreciate your time. Thanks a lot for your
suggestions.

One thing I'm worried about here. In previous mail, I mentioned the
"distance at start" and "ref at t=0" is negative. What does the negative
value signify, I mean how can distance be negative ? Is is due to my poorly
given vector definition or something else ?



It's a vector quantity.  It can be positive or negative depending on how you 
define the groups and what their positions are.  And you're telling grompp to 
pull along the negative-z dimension.


-Justin


On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:




On 5/11/17 9:21 AM, abhisek Mondal wrote:


On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
wrote:

Hi,


Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry   = direction ; simple distance increase
pull_dim   = Y Y Y ; not to allow ligand move along other
dir
pull_rate1 = 0.0
pull_k1   = 1000   ; kJ mol^-1 nm^-2
pull_start   = yes   ; define initial COM distance > 0
pull_vec1   = 0 0 -1



Note that with "direction" geometry, only pull_vec1 is acting.  pull_dim
is ignored.

The ligand was previously moving along x,y direction when I was using

pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
as
vector  and pull_rate1=0.0, so that it does not move much. But at the end
of a 10ns run, I see that the ligand is still moving as it was earlier.

It shows me:

 Pull group  natoms  pbc atom  distance at start reference at t=0
   0  1132936665
   159  1618  -1.555-1.555
Is it ok withe negative value ? Anyway this setup is not working.



Again you're trying to just apply the restraint to one dimension and it
looks to be fairly arbitrary.  I already suggested using the vector
connecting the ligand COM with the binding site residues' COM and using
that as pull_vec1.  Draw it out.  It makes a lot more sense than trying to
restrain only along one axis, which as I have said before, makes no sense
in this case.

-Justin



I have choose my reaction coordinate to be along -Z axis and want to
apply
biasing potential accordingly with restraining the ligand movement. Can
you
please suggest where am I failing with this code ?

Thank you.



On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul  wrote:




On 5/8/17 10:00 AM, abhisek Mondal wrote:

On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:





On 5/7/17 1:57 AM, abhisek Mondal wrote:

Hi,



For your ease of understanding regarding what is happening during
this
above said umbrella-mdrun, I have shared the trajectory video file
the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Is this normal given that the mdp code being used ? I basically have
no
idea with this step, so please help me out. I'm using gromacs-4.6.2.


Your setup is incorrect.  You're applying a biasing potential only


along
z, so the ligand can move freely along x and y.  A protein-ligand
complex
has spherical symmetry, so you should set the reaction coordinate to
the
vector connecting the ligand with some suitable subset of interacting
protein residues.




I don't get it.
We are trying not to move our configuration (generated after pulling
simulation) along the reaction coordinate, so for restraining we are
supposed to set pull_rate1=0.0.



Of course.  But you said set pull_k = 0 which does not make sense.  The
pulling rate *is* zero during umbrella sampling (no net displacement,
restrain to the specified distance along the reaction coordinate) and
pulling force constant should be non-zero.

If applying biasing potential only along z is causing movement along x
and


y then what if we apply the biasing potential along x,y,z ? Will it
cause
any good in restraining the ligand?


This is how it should be done.  The reaction coordinate should be

suitably defined based on the geometry of the system.  As I suggested
before, choose some representative residues in the active site as one
group
and the ligand as the other.  Thus defines the reaction coordinate
without
any presupposition of anything being aligned with a Cartesian axis,
which
is rarely the case.

Moreover, you said previously "A protein-ligand complex has spherical


symmetry, so you should set the reaction coordinate to the vector
connecting the ligand with some suitable subset of interacting protein
residues.". It is really unclear to me, could you 

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Alright. I'm trying as per your advice. Actually my system is pretty big
and due to constraint of computation power it is taking me more time to
test vector setup. I really appreciate your time. Thanks a lot for your
suggestions.

One thing I'm worried about here. In previous mail, I mentioned the
"distance at start" and "ref at t=0" is negative. What does the negative
value signify, I mean how can distance be negative ? Is is due to my poorly
given vector definition or something else ?

On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul  wrote:

>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in this step. I have modified the code as:
>>> ; Pull code
>>> pull= umbrella
>>> pull_ngroups= 1
>>> pull_group0 = Protein_chain_A
>>> pull_group1 = ACO
>>> pull_geometry   = direction ; simple distance increase
>>> pull_dim   = Y Y Y ; not to allow ligand move along other
>>> dir
>>> pull_rate1 = 0.0
>>> pull_k1   = 1000   ; kJ mol^-1 nm^-2
>>> pull_start   = yes   ; define initial COM distance > 0
>>> pull_vec1   = 0 0 -1
>>>
>>>
> Note that with "direction" geometry, only pull_vec1 is acting.  pull_dim
> is ignored.
>
> The ligand was previously moving along x,y direction when I was using
>>> pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
>>> as
>>> vector  and pull_rate1=0.0, so that it does not move much. But at the end
>>> of a 10ns run, I see that the ligand is still moving as it was earlier.
>>>
>>> It shows me:
>>  Pull group  natoms  pbc atom  distance at start reference at t=0
>>0  1132936665
>>159  1618  -1.555-1.555
>> Is it ok withe negative value ? Anyway this setup is not working.
>>
>>
> Again you're trying to just apply the restraint to one dimension and it
> looks to be fairly arbitrary.  I already suggested using the vector
> connecting the ligand COM with the binding site residues' COM and using
> that as pull_vec1.  Draw it out.  It makes a lot more sense than trying to
> restrain only along one axis, which as I have said before, makes no sense
> in this case.
>
> -Justin
>
>
>>> I have choose my reaction coordinate to be along -Z axis and want to
>>> apply
>>> biasing potential accordingly with restraining the ligand movement. Can
>>> you
>>> please suggest where am I failing with this code ?
>>>
>>> Thank you.
>>>
>>>
>>>
>>> On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul  wrote:
>>>
>>>

 On 5/8/17 10:00 AM, abhisek Mondal wrote:

 On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:
>
>
>
>> On 5/7/17 1:57 AM, abhisek Mondal wrote:
>>
>> Hi,
>>
>>>
>>> For your ease of understanding regarding what is happening during
>>> this
>>> above said umbrella-mdrun, I have shared the trajectory video file
>>> the
>>> following link.
>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>>
>>> Is this normal given that the mdp code being used ? I basically have
>>> no
>>> idea with this step, so please help me out. I'm using gromacs-4.6.2.
>>>
>>>
>>> Your setup is incorrect.  You're applying a biasing potential only
>>>
>> along
>> z, so the ligand can move freely along x and y.  A protein-ligand
>> complex
>> has spherical symmetry, so you should set the reaction coordinate to
>> the
>> vector connecting the ligand with some suitable subset of interacting
>> protein residues.
>>
>>
>
> I don't get it.
> We are trying not to move our configuration (generated after pulling
> simulation) along the reaction coordinate, so for restraining we are
> supposed to set pull_rate1=0.0.
>
>
 Of course.  But you said set pull_k = 0 which does not make sense.  The
 pulling rate *is* zero during umbrella sampling (no net displacement,
 restrain to the specified distance along the reaction coordinate) and
 pulling force constant should be non-zero.

 If applying biasing potential only along z is causing movement along x
 and

> y then what if we apply the biasing potential along x,y,z ? Will it
> cause
> any good in restraining the ligand?
>
>
> This is how it should be done.  The reaction coordinate should be
 suitably defined based on the geometry of the system.  As I suggested
 before, choose some representative residues in the active site as one
 group
 and the ligand as the other.  Thus defines the reaction coordinate
 without
 any presupposition of anything being aligned with a 

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/11/17 9:21 AM, abhisek Mondal wrote:

On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
wrote:


Hi,

Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry   = direction ; simple distance increase
pull_dim   = Y Y Y ; not to allow ligand move along other
dir
pull_rate1 = 0.0
pull_k1   = 1000   ; kJ mol^-1 nm^-2
pull_start   = yes   ; define initial COM distance > 0
pull_vec1   = 0 0 -1



Note that with "direction" geometry, only pull_vec1 is acting.  pull_dim is 
ignored.


The ligand was previously moving along x,y direction when I was using
pull_dim  = N N Y. So I changed it to Y in all direction and provided 0 as
vector  and pull_rate1=0.0, so that it does not move much. But at the end
of a 10ns run, I see that the ligand is still moving as it was earlier.


It shows me:
 Pull group  natoms  pbc atom  distance at start reference at t=0
   0  1132936665
   159  1618  -1.555-1.555
Is it ok withe negative value ? Anyway this setup is not working.



Again you're trying to just apply the restraint to one dimension and it looks to 
be fairly arbitrary.  I already suggested using the vector connecting the ligand 
COM with the binding site residues' COM and using that as pull_vec1.  Draw it 
out.  It makes a lot more sense than trying to restrain only along one axis, 
which as I have said before, makes no sense in this case.


-Justin



I have choose my reaction coordinate to be along -Z axis and want to apply
biasing potential accordingly with restraining the ligand movement. Can you
please suggest where am I failing with this code ?

Thank you.



On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul  wrote:




On 5/8/17 10:00 AM, abhisek Mondal wrote:


On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:




On 5/7/17 1:57 AM, abhisek Mondal wrote:

Hi,


For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Is this normal given that the mdp code being used ? I basically have no
idea with this step, so please help me out. I'm using gromacs-4.6.2.


Your setup is incorrect.  You're applying a biasing potential only

along
z, so the ligand can move freely along x and y.  A protein-ligand
complex
has spherical symmetry, so you should set the reaction coordinate to the
vector connecting the ligand with some suitable subset of interacting
protein residues.




I don't get it.
We are trying not to move our configuration (generated after pulling
simulation) along the reaction coordinate, so for restraining we are
supposed to set pull_rate1=0.0.



Of course.  But you said set pull_k = 0 which does not make sense.  The
pulling rate *is* zero during umbrella sampling (no net displacement,
restrain to the specified distance along the reaction coordinate) and
pulling force constant should be non-zero.

If applying biasing potential only along z is causing movement along x and

y then what if we apply the biasing potential along x,y,z ? Will it cause
any good in restraining the ligand?



This is how it should be done.  The reaction coordinate should be
suitably defined based on the geometry of the system.  As I suggested
before, choose some representative residues in the active site as one group
and the ligand as the other.  Thus defines the reaction coordinate without
any presupposition of anything being aligned with a Cartesian axis, which
is rarely the case.

Moreover, you said previously "A protein-ligand complex has spherical

symmetry, so you should set the reaction coordinate to the vector
connecting the ligand with some suitable subset of interacting protein
residues.". It is really unclear to me, could you please give me some
examples to understand it more simply? I had pulled the ligand along -z
axis, doesn't it mean that the reaction coordinate is to be that way ?
The
fact that I'm struggling with is to restrain the pull configurations for
further sampling.



The reaction coordinate is whatever you define it to be.  Whether or not
pulling along the z-axis makes sense depends on the orientation of the
system and the intrinsic geometry.  In your case, it doesn't make sense.
In my case (the tutorial, the unidirectional growth of an amyloid fibril)
it does make sense to use a single Cartesian axis for the SMD portion and
subsequent umbrella sampling.

I'm really a beginner, so maybe I'm asking stupid questions. Please give

me
some advise. I'm really unable to decipher the scenario in comparison to
your amyloid 

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal 
wrote:

> Hi,
>
> Thank you for the explanation. It really cleared some concepts. But I'm
> still having my ligand moving in this step. I have modified the code as:
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = Protein_chain_A
> pull_group1 = ACO
> pull_geometry   = direction ; simple distance increase
> pull_dim   = Y Y Y ; not to allow ligand move along other
> dir
> pull_rate1 = 0.0
> pull_k1   = 1000   ; kJ mol^-1 nm^-2
> pull_start   = yes   ; define initial COM distance > 0
> pull_vec1   = 0 0 -1
>
> The ligand was previously moving along x,y direction when I was using
> pull_dim  = N N Y. So I changed it to Y in all direction and provided 0 as
> vector  and pull_rate1=0.0, so that it does not move much. But at the end
> of a 10ns run, I see that the ligand is still moving as it was earlier.
>
It shows me:
 Pull group  natoms  pbc atom  distance at start reference at t=0
   0  1132936665
   159  1618  -1.555-1.555
Is it ok withe negative value ? Anyway this setup is not working.

>
> I have choose my reaction coordinate to be along -Z axis and want to apply
> biasing potential accordingly with restraining the ligand movement. Can you
> please suggest where am I failing with this code ?
>
> Thank you.
>
>
>
> On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/8/17 10:00 AM, abhisek Mondal wrote:
>>
>>> On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:
>>>
>>>

 On 5/7/17 1:57 AM, abhisek Mondal wrote:

 Hi,
>
> For your ease of understanding regarding what is happening during this
> above said umbrella-mdrun, I have shared the trajectory video file the
> following link.
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>
> Is this normal given that the mdp code being used ? I basically have no
> idea with this step, so please help me out. I'm using gromacs-4.6.2.
>
>
> Your setup is incorrect.  You're applying a biasing potential only
 along
 z, so the ligand can move freely along x and y.  A protein-ligand
 complex
 has spherical symmetry, so you should set the reaction coordinate to the
 vector connecting the ligand with some suitable subset of interacting
 protein residues.

>>>
>>>
>>> I don't get it.
>>> We are trying not to move our configuration (generated after pulling
>>> simulation) along the reaction coordinate, so for restraining we are
>>> supposed to set pull_rate1=0.0.
>>>
>>
>> Of course.  But you said set pull_k = 0 which does not make sense.  The
>> pulling rate *is* zero during umbrella sampling (no net displacement,
>> restrain to the specified distance along the reaction coordinate) and
>> pulling force constant should be non-zero.
>>
>> If applying biasing potential only along z is causing movement along x and
>>> y then what if we apply the biasing potential along x,y,z ? Will it cause
>>> any good in restraining the ligand?
>>>
>>>
>> This is how it should be done.  The reaction coordinate should be
>> suitably defined based on the geometry of the system.  As I suggested
>> before, choose some representative residues in the active site as one group
>> and the ligand as the other.  Thus defines the reaction coordinate without
>> any presupposition of anything being aligned with a Cartesian axis, which
>> is rarely the case.
>>
>> Moreover, you said previously "A protein-ligand complex has spherical
>>> symmetry, so you should set the reaction coordinate to the vector
>>> connecting the ligand with some suitable subset of interacting protein
>>> residues.". It is really unclear to me, could you please give me some
>>> examples to understand it more simply? I had pulled the ligand along -z
>>> axis, doesn't it mean that the reaction coordinate is to be that way ?
>>> The
>>> fact that I'm struggling with is to restrain the pull configurations for
>>> further sampling.
>>>
>>>
>> The reaction coordinate is whatever you define it to be.  Whether or not
>> pulling along the z-axis makes sense depends on the orientation of the
>> system and the intrinsic geometry.  In your case, it doesn't make sense.
>> In my case (the tutorial, the unidirectional growth of an amyloid fibril)
>> it does make sense to use a single Cartesian axis for the SMD portion and
>> subsequent umbrella sampling.
>>
>> I'm really a beginner, so maybe I'm asking stupid questions. Please give
>>> me
>>> some advise. I'm really unable to decipher the scenario in comparison to
>>> your amyloid article in JPCB.
>>>
>>>
>> You should read the article to understand why I did what I did in the
>> tutorial, and then move on to reading articles that are more similar to
>> your case.  These will 

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Hi,

Thank you for the explanation. It really cleared some concepts. But I'm
still having my ligand moving in this step. I have modified the code as:
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry   = direction ; simple distance increase
pull_dim   = Y Y Y ; not to allow ligand move along other
dir
pull_rate1 = 0.0
pull_k1   = 1000   ; kJ mol^-1 nm^-2
pull_start   = yes   ; define initial COM distance > 0
pull_vec1   = 0 0 -1

The ligand was previously moving along x,y direction when I was using
pull_dim  = N N Y. So I changed it to Y in all direction and provided 0 as
vector  and pull_rate1=0.0, so that it does not move much. But at the end
of a 10ns run, I see that the ligand is still moving as it was earlier.

I have choose my reaction coordinate to be along -Z axis and want to apply
biasing potential accordingly with restraining the ligand movement. Can you
please suggest where am I failing with this code ?

Thank you.



On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul  wrote:

>
>
> On 5/8/17 10:00 AM, abhisek Mondal wrote:
>
>> On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/7/17 1:57 AM, abhisek Mondal wrote:
>>>
>>> Hi,

 For your ease of understanding regarding what is happening during this
 above said umbrella-mdrun, I have shared the trajectory video file the
 following link.
 https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

 Is this normal given that the mdp code being used ? I basically have no
 idea with this step, so please help me out. I'm using gromacs-4.6.2.


 Your setup is incorrect.  You're applying a biasing potential only along
>>> z, so the ligand can move freely along x and y.  A protein-ligand complex
>>> has spherical symmetry, so you should set the reaction coordinate to the
>>> vector connecting the ligand with some suitable subset of interacting
>>> protein residues.
>>>
>>
>>
>> I don't get it.
>> We are trying not to move our configuration (generated after pulling
>> simulation) along the reaction coordinate, so for restraining we are
>> supposed to set pull_rate1=0.0.
>>
>
> Of course.  But you said set pull_k = 0 which does not make sense.  The
> pulling rate *is* zero during umbrella sampling (no net displacement,
> restrain to the specified distance along the reaction coordinate) and
> pulling force constant should be non-zero.
>
> If applying biasing potential only along z is causing movement along x and
>> y then what if we apply the biasing potential along x,y,z ? Will it cause
>> any good in restraining the ligand?
>>
>>
> This is how it should be done.  The reaction coordinate should be suitably
> defined based on the geometry of the system.  As I suggested before, choose
> some representative residues in the active site as one group and the ligand
> as the other.  Thus defines the reaction coordinate without any
> presupposition of anything being aligned with a Cartesian axis, which is
> rarely the case.
>
> Moreover, you said previously "A protein-ligand complex has spherical
>> symmetry, so you should set the reaction coordinate to the vector
>> connecting the ligand with some suitable subset of interacting protein
>> residues.". It is really unclear to me, could you please give me some
>> examples to understand it more simply? I had pulled the ligand along -z
>> axis, doesn't it mean that the reaction coordinate is to be that way ? The
>> fact that I'm struggling with is to restrain the pull configurations for
>> further sampling.
>>
>>
> The reaction coordinate is whatever you define it to be.  Whether or not
> pulling along the z-axis makes sense depends on the orientation of the
> system and the intrinsic geometry.  In your case, it doesn't make sense.
> In my case (the tutorial, the unidirectional growth of an amyloid fibril)
> it does make sense to use a single Cartesian axis for the SMD portion and
> subsequent umbrella sampling.
>
> I'm really a beginner, so maybe I'm asking stupid questions. Please give me
>> some advise. I'm really unable to decipher the scenario in comparison to
>> your amyloid article in JPCB.
>>
>>
> You should read the article to understand why I did what I did in the
> tutorial, and then move on to reading articles that are more similar to
> your case.  These will be much more relevant to what you're doing.
>
> -Justin
>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> 

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/8/17 10:00 AM, abhisek Mondal wrote:

On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:




On 5/7/17 1:57 AM, abhisek Mondal wrote:


Hi,

For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Is this normal given that the mdp code being used ? I basically have no
idea with this step, so please help me out. I'm using gromacs-4.6.2.



Your setup is incorrect.  You're applying a biasing potential only along
z, so the ligand can move freely along x and y.  A protein-ligand complex
has spherical symmetry, so you should set the reaction coordinate to the
vector connecting the ligand with some suitable subset of interacting
protein residues.



I don't get it.
We are trying not to move our configuration (generated after pulling
simulation) along the reaction coordinate, so for restraining we are
supposed to set pull_rate1=0.0.


Of course.  But you said set pull_k = 0 which does not make sense.  The pulling 
rate *is* zero during umbrella sampling (no net displacement, restrain to the 
specified distance along the reaction coordinate) and pulling force constant 
should be non-zero.



If applying biasing potential only along z is causing movement along x and
y then what if we apply the biasing potential along x,y,z ? Will it cause
any good in restraining the ligand?



This is how it should be done.  The reaction coordinate should be suitably 
defined based on the geometry of the system.  As I suggested before, choose some 
representative residues in the active site as one group and the ligand as the 
other.  Thus defines the reaction coordinate without any presupposition of 
anything being aligned with a Cartesian axis, which is rarely the case.



Moreover, you said previously "A protein-ligand complex has spherical
symmetry, so you should set the reaction coordinate to the vector
connecting the ligand with some suitable subset of interacting protein
residues.". It is really unclear to me, could you please give me some
examples to understand it more simply? I had pulled the ligand along -z
axis, doesn't it mean that the reaction coordinate is to be that way ? The
fact that I'm struggling with is to restrain the pull configurations for
further sampling.



The reaction coordinate is whatever you define it to be.  Whether or not pulling 
along the z-axis makes sense depends on the orientation of the system and the 
intrinsic geometry.  In your case, it doesn't make sense.  In my case (the 
tutorial, the unidirectional growth of an amyloid fibril) it does make sense to 
use a single Cartesian axis for the SMD portion and subsequent umbrella sampling.



I'm really a beginner, so maybe I'm asking stupid questions. Please give me
some advise. I'm really unable to decipher the scenario in comparison to
your amyloid article in JPCB.



You should read the article to understand why I did what I did in the tutorial, 
and then move on to reading articles that are more similar to your case.  These 
will be much more relevant to what you're doing.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Ligand Boron parameters

[Justin Lemkul]

On 5/8/17 9:04 AM, Pedro Fernandes wrote:

Good afternoon,

I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a 
boron atom.
Can anyone help me or give me some information how can I do the 
parameterization of the ligand.



The details will depend on the force field you've chosen to use for the protein. 
 Factoring into that decision is how easy it will be to parametrize a ligand 
with boron, which none of the commonly used biomolecular force fields have. 
You'll be starting from absolute scratch with that atom type so you will want to 
be well versed in force field parametrization methods (beware: expert topic ahead).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul  wrote:

>
>
> On 5/7/17 1:57 AM, abhisek Mondal wrote:
>
>> Hi,
>>
>> For your ease of understanding regarding what is happening during this
>> above said umbrella-mdrun, I have shared the trajectory video file the
>> following link.
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>> Is this normal given that the mdp code being used ? I basically have no
>> idea with this step, so please help me out. I'm using gromacs-4.6.2.
>>
>>
> Your setup is incorrect.  You're applying a biasing potential only along
> z, so the ligand can move freely along x and y.  A protein-ligand complex
> has spherical symmetry, so you should set the reaction coordinate to the
> vector connecting the ligand with some suitable subset of interacting
> protein residues.


I don't get it.
We are trying not to move our configuration (generated after pulling
simulation) along the reaction coordinate, so for restraining we are
supposed to set pull_rate1=0.0.
If applying biasing potential only along z is causing movement along x and
y then what if we apply the biasing potential along x,y,z ? Will it cause
any good in restraining the ligand?

Moreover, you said previously "A protein-ligand complex has spherical
symmetry, so you should set the reaction coordinate to the vector
connecting the ligand with some suitable subset of interacting protein
residues.". It is really unclear to me, could you please give me some
examples to understand it more simply? I had pulled the ligand along -z
axis, doesn't it mean that the reaction coordinate is to be that way ? The
fact that I'm struggling with is to restrain the pull configurations for
further sampling.

I'm really a beginner, so maybe I'm asking stupid questions. Please give me
some advise. I'm really unable to decipher the scenario in comparison to
your amyloid article in JPCB.


  You're following the tutorial too literally and that's not correct.  Also
> do not restrain the protein (I say this weekly; not enough people are
> reading the details of the tutorial and associated paper and just copying
> .mdp settings...)
>
> -Justin
>
>
>> On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal 
>> wrote:
>>
>> Hi,
>>>
>>> I have completed pulling as per the tutorial stated. But having a strange
>>> issue during umbrella sampling. When I execute:
>>> *mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
>>> pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
>>>
>>> The gro file generated at the end shows the ligand is way far compared to
>>> starting position, as if another pulling is done !
>>> Please suggest me a way to tackle this issue. If this thing happens to
>>> all
>>> the configurations generated during pulling then how am I supposed to get
>>> the PMF ?
>>>
>>> The md_umbrella.mdp I'm using is:
>>> title   = Umbrella pulling simulation
>>> define  = -DPOSRES
>>> ; Run parameters
>>> integrator  = md
>>> dt  = 0.002
>>> tinit   = 0
>>> nsteps  = 500   ; 10 ns
>>> nstcomm = 10
>>> ; Output parameters
>>> nstxout = 5 ; every 100 ps
>>> nstvout = 5
>>> nstfout = 5000
>>> nstxtcout   = 5000 ; every 10 ps
>>> nstenergy   = 5000
>>> ; Bond parameters
>>> constraint_algorithm= lincs
>>> constraints = all-bonds
>>> continuation= yes
>>> ; Single-range cutoff scheme
>>> nstlist = 5
>>> ns_type = grid
>>> rlist   = 1.4
>>> rcoulomb= 1.4
>>> rvdw= 1.4
>>> ; PME electrostatics parameters
>>> coulombtype = PME
>>> fourierspacing  = 0.12
>>> fourier_nx = 0
>>> fourier_ny = 0
>>> fourier_nz = 0
>>> pme_order = 4
>>> ewald_rtol = 1e-5
>>> optimize_fft= yes
>>> ; Berendsen temperature coupling is on in two groups
>>> Tcoupl  = Nose-Hoover
>>> tc_grps = Protein   Non-Protein
>>> tau_t   = 0.5 0.5
>>> ref_t   = 310 310
>>> ; Pressure coupling is on
>>> Pcoupl  = Parrinello-Rahman
>>> pcoupltype = isotropic
>>> tau_p   = 1.0
>>> compressibility = 4.5e-5
>>> ref_p   = 1.0
>>> refcoord_scaling = com
>>> ; Generate velocities is off
>>> gen_vel = no
>>> ; Periodic boundary conditions are on in all directions
>>> pbc = xyz
>>> ; Long-range dispersion correction
>>> DispCorr= EnerPres
>>> ; Pull code
>>> pull= umbrella
>>> pull_ngroups= 1
>>> pull_group0 = Protein_chain_A
>>> pull_group1 = ACO
>>> pull_geometry   = direction
>>> pull_dim= N N Y ; pulling in Z dimension
>>> pull_rate1  = 0.0
>>> pull_k1 = 1000   ; kJ mol^-1 nm^-2
>>> pull_start  = yes   ; define initial COM distance > 0
>>> pull_vec1   = 0 0 -1
>>>
>>> My question is despite the pull_rate1 being 0.0, why the ligand is moving
>>> ? Is it the pull_start or something else I'm missing here resulting in
>>> such
>>> 

[gmx-users] Ligand Boron parameters

[Pedro Fernandes]

Good afternoon,

I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a 
boron atom. 
Can anyone help me or give me some information how can I do the 
parameterization of the ligand.

Best Regards,
Pedro Fernandes
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/7/17 2:22 PM, abhisek Mondal wrote:

Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.

You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't move this
way.


If you set pull_k1 to zero, it won't accomplish anything at all.  You'll have no 
biasing force.



You mentioned that during this run we want to restrain the ligand or don't
want to change the configuration generated by pulling simulation.
Is this approach right?



I don't understand the second question.

-Justin




On May 7, 2017 11:37 PM, "Justin Lemkul"  wrote:



On 5/7/17 1:57 AM, abhisek Mondal wrote:


Hi,

For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Is this normal given that the mdp code being used ? I basically have no
idea with this step, so please help me out. I'm using gromacs-4.6.2.



Your setup is incorrect.  You're applying a biasing potential only along z,
so the ligand can move freely along x and y.  A protein-ligand complex has
spherical symmetry, so you should set the reaction coordinate to the vector
connecting the ligand with some suitable subset of interacting protein
residues.  You're following the tutorial too literally and that's not
correct.  Also do not restrain the protein (I say this weekly; not enough
people are reading the details of the tutorial and associated paper and
just copying .mdp settings...)

-Justin



On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal 
wrote:

Hi,


I have completed pulling as per the tutorial stated. But having a strange
issue during umbrella sampling. When I execute:
*mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
pullf-umbrella8.xvg -px pullx-umbrella8.xvg*

The gro file generated at the end shows the ligand is way far compared to
starting position, as if another pulling is done !
Please suggest me a way to tackle this issue. If this thing happens to all
the configurations generated during pulling then how am I supposed to get
the PMF ?

The md_umbrella.mdp I'm using is:
title   = Umbrella pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 500   ; 10 ns
nstcomm = 10
; Output parameters
nstxout = 5 ; every 100 ps
nstvout = 5
nstfout = 5000
nstxtcout   = 5000 ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein   Non-Protein
tau_t   = 0.5 0.5
ref_t   = 310 310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry   = direction
pull_dim= N N Y ; pulling in Z dimension
pull_rate1  = 0.0
pull_k1 = 1000   ; kJ mol^-1 nm^-2
pull_start  = yes   ; define initial COM distance > 0
pull_vec1   = 0 0 -1

My question is despite the pull_rate1 being 0.0, why the ligand is moving
? Is it the pull_start or something else I'm missing here resulting in
such
a crash ?

Your suggestions will be highly appreciated.
Thank you.

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*








--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? 

Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Hello Justin,
Thank you for the explanation. I'm really new to the field so choosing
factors in a bit confusion.

You said in this set up the ligand can still move around X and Y direction.
My question is what if I set pull_k1=0? The ligand also won't move this
way.
You mentioned that during this run we want to restrain the ligand or don't
want to change the configuration generated by pulling simulation.
Is this approach right?



On May 7, 2017 11:37 PM, "Justin Lemkul"  wrote:



On 5/7/17 1:57 AM, abhisek Mondal wrote:

> Hi,
>
> For your ease of understanding regarding what is happening during this
> above said umbrella-mdrun, I have shared the trajectory video file the
> following link.
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>
> Is this normal given that the mdp code being used ? I basically have no
> idea with this step, so please help me out. I'm using gromacs-4.6.2.
>
>
Your setup is incorrect.  You're applying a biasing potential only along z,
so the ligand can move freely along x and y.  A protein-ligand complex has
spherical symmetry, so you should set the reaction coordinate to the vector
connecting the ligand with some suitable subset of interacting protein
residues.  You're following the tutorial too literally and that's not
correct.  Also do not restrain the protein (I say this weekly; not enough
people are reading the details of the tutorial and associated paper and
just copying .mdp settings...)

-Justin


> On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal 
> wrote:
>
> Hi,
>>
>> I have completed pulling as per the tutorial stated. But having a strange
>> issue during umbrella sampling. When I execute:
>> *mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
>> pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
>>
>> The gro file generated at the end shows the ligand is way far compared to
>> starting position, as if another pulling is done !
>> Please suggest me a way to tackle this issue. If this thing happens to all
>> the configurations generated during pulling then how am I supposed to get
>> the PMF ?
>>
>> The md_umbrella.mdp I'm using is:
>> title   = Umbrella pulling simulation
>> define  = -DPOSRES
>> ; Run parameters
>> integrator  = md
>> dt  = 0.002
>> tinit   = 0
>> nsteps  = 500   ; 10 ns
>> nstcomm = 10
>> ; Output parameters
>> nstxout = 5 ; every 100 ps
>> nstvout = 5
>> nstfout = 5000
>> nstxtcout   = 5000 ; every 10 ps
>> nstenergy   = 5000
>> ; Bond parameters
>> constraint_algorithm= lincs
>> constraints = all-bonds
>> continuation= yes
>> ; Single-range cutoff scheme
>> nstlist = 5
>> ns_type = grid
>> rlist   = 1.4
>> rcoulomb= 1.4
>> rvdw= 1.4
>> ; PME electrostatics parameters
>> coulombtype = PME
>> fourierspacing  = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 4
>> ewald_rtol = 1e-5
>> optimize_fft= yes
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl  = Nose-Hoover
>> tc_grps = Protein   Non-Protein
>> tau_t   = 0.5 0.5
>> ref_t   = 310 310
>> ; Pressure coupling is on
>> Pcoupl  = Parrinello-Rahman
>> pcoupltype = isotropic
>> tau_p   = 1.0
>> compressibility = 4.5e-5
>> ref_p   = 1.0
>> refcoord_scaling = com
>> ; Generate velocities is off
>> gen_vel = no
>> ; Periodic boundary conditions are on in all directions
>> pbc = xyz
>> ; Long-range dispersion correction
>> DispCorr= EnerPres
>> ; Pull code
>> pull= umbrella
>> pull_ngroups= 1
>> pull_group0 = Protein_chain_A
>> pull_group1 = ACO
>> pull_geometry   = direction
>> pull_dim= N N Y ; pulling in Z dimension
>> pull_rate1  = 0.0
>> pull_k1 = 1000   ; kJ mol^-1 nm^-2
>> pull_start  = yes   ; define initial COM distance > 0
>> pull_vec1   = 0 0 -1
>>
>> My question is despite the pull_rate1 being 0.0, why the ligand is moving
>> ? Is it the pull_start or something else I'm missing here resulting in
>> such
>> a crash ?
>>
>> Your suggestions will be highly appreciated.
>> Thank you.
>>
>> --
>> Abhisek Mondal
>>
>> *Senior Research Fellow*
>>
>> *Structural Biology and Bioinformatics Division*
>> *CSIR-Indian Institute of Chemical Biology*
>>
>> *Kolkata 700032*
>>
>> *INDIA*
>>
>>
>
>
>
-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/7/17 1:57 AM, abhisek Mondal wrote:

Hi,

For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Is this normal given that the mdp code being used ? I basically have no
idea with this step, so please help me out. I'm using gromacs-4.6.2.



Your setup is incorrect.  You're applying a biasing potential only along z, so 
the ligand can move freely along x and y.  A protein-ligand complex has 
spherical symmetry, so you should set the reaction coordinate to the vector 
connecting the ligand with some suitable subset of interacting protein residues. 
 You're following the tutorial too literally and that's not correct.  Also do 
not restrain the protein (I say this weekly; not enough people are reading the 
details of the tutorial and associated paper and just copying .mdp settings...)


-Justin



On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal 
wrote:


Hi,

I have completed pulling as per the tutorial stated. But having a strange
issue during umbrella sampling. When I execute:
*mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
The gro file generated at the end shows the ligand is way far compared to
starting position, as if another pulling is done !
Please suggest me a way to tackle this issue. If this thing happens to all
the configurations generated during pulling then how am I supposed to get
the PMF ?

The md_umbrella.mdp I'm using is:
title   = Umbrella pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 500   ; 10 ns
nstcomm = 10
; Output parameters
nstxout = 5 ; every 100 ps
nstvout = 5
nstfout = 5000
nstxtcout   = 5000 ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein   Non-Protein
tau_t   = 0.5 0.5
ref_t   = 310 310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry   = direction
pull_dim= N N Y ; pulling in Z dimension
pull_rate1  = 0.0
pull_k1 = 1000   ; kJ mol^-1 nm^-2
pull_start  = yes   ; define initial COM distance > 0
pull_vec1   = 0 0 -1

My question is despite the pull_rate1 being 0.0, why the ligand is moving
? Is it the pull_start or something else I'm missing here resulting in such
a crash ?

Your suggestions will be highly appreciated.
Thank you.

--
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*







--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Hi,

For your ease of understanding regarding what is happening during this
above said umbrella-mdrun, I have shared the trajectory video file the
following link.
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Is this normal given that the mdp code being used ? I basically have no
idea with this step, so please help me out. I'm using gromacs-4.6.2.


On Sun, May 7, 2017 at 9:57 AM, abhisek Mondal 
wrote:

> Hi,
>
> I have completed pulling as per the tutorial stated. But having a strange
> issue during umbrella sampling. When I execute:
> *mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
> pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
> The gro file generated at the end shows the ligand is way far compared to
> starting position, as if another pulling is done !
> Please suggest me a way to tackle this issue. If this thing happens to all
> the configurations generated during pulling then how am I supposed to get
> the PMF ?
>
> The md_umbrella.mdp I'm using is:
> title   = Umbrella pulling simulation
> define  = -DPOSRES
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 500   ; 10 ns
> nstcomm = 10
> ; Output parameters
> nstxout = 5 ; every 100 ps
> nstvout = 5
> nstfout = 5000
> nstxtcout   = 5000 ; every 10 ps
> nstenergy   = 5000
> ; Bond parameters
> constraint_algorithm= lincs
> constraints = all-bonds
> continuation= yes
> ; Single-range cutoff scheme
> nstlist = 5
> ns_type = grid
> rlist   = 1.4
> rcoulomb= 1.4
> rvdw= 1.4
> ; PME electrostatics parameters
> coulombtype = PME
> fourierspacing  = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft= yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl  = Nose-Hoover
> tc_grps = Protein   Non-Protein
> tau_t   = 0.5 0.5
> ref_t   = 310 310
> ; Pressure coupling is on
> Pcoupl  = Parrinello-Rahman
> pcoupltype = isotropic
> tau_p   = 1.0
> compressibility = 4.5e-5
> ref_p   = 1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
> ; Long-range dispersion correction
> DispCorr= EnerPres
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = Protein_chain_A
> pull_group1 = ACO
> pull_geometry   = direction
> pull_dim= N N Y ; pulling in Z dimension
> pull_rate1  = 0.0
> pull_k1 = 1000   ; kJ mol^-1 nm^-2
> pull_start  = yes   ; define initial COM distance > 0
> pull_vec1   = 0 0 -1
>
> My question is despite the pull_rate1 being 0.0, why the ligand is moving
> ? Is it the pull_start or something else I'm missing here resulting in such
> a crash ?
>
> Your suggestions will be highly appreciated.
> Thank you.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Hi,

I have completed pulling as per the tutorial stated. But having a strange
issue during umbrella sampling. When I execute:
*mpirun -np 320 /app/gromacs462/bin/mdrun_mpi -v -deffnm umbrella8 -pf
pullf-umbrella8.xvg -px pullx-umbrella8.xvg*
The gro file generated at the end shows the ligand is way far compared to
starting position, as if another pulling is done !
Please suggest me a way to tackle this issue. If this thing happens to all
the configurations generated during pulling then how am I supposed to get
the PMF ?

The md_umbrella.mdp I'm using is:
title   = Umbrella pulling simulation
define  = -DPOSRES
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 500   ; 10 ns
nstcomm = 10
; Output parameters
nstxout = 5 ; every 100 ps
nstvout = 5
nstfout = 5000
nstxtcout   = 5000 ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = Protein   Non-Protein
tau_t   = 0.5 0.5
ref_t   = 310 310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = Protein_chain_A
pull_group1 = ACO
pull_geometry   = direction
pull_dim= N N Y ; pulling in Z dimension
pull_rate1  = 0.0
pull_k1 = 1000   ; kJ mol^-1 nm^-2
pull_start  = yes   ; define initial COM distance > 0
pull_vec1   = 0 0 -1

My question is despite the pull_rate1 being 0.0, why the ligand is moving ?
Is it the pull_start or something else I'm missing here resulting in such a
crash ?

Your suggestions will be highly appreciated.
Thank you.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
Gromacs Users mailing list

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Re: [gmx-users] Ligand simulation

[Mark Abraham]

Hi,

On Wed, 5 Apr 2017 08:49 RAHUL SURESH  wrote:

> for Command
>
>
>
> *gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
> I get the following error.
>
>
> *Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
> - 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
> (H82 - 2H8)*
>
> Is it really an issue or can I use -maxwarn?
>

Only you can know whether the difference in naming reflects your intent, or
not. Why did you generate the topology from a coordinate file that is
different from what you are using with grompp?

Mark

--
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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Re: [gmx-users] Ligand simulation

[abhisek Mondal]

Check the total number of atoms at the top of topology files. If you have
made a complex manually then the numbers had to be accounted for.

On Wed, Apr 5, 2017 at 12:18 PM, RAHUL SURESH 
wrote:

> for Command
>
>
>
> *gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
> I get the following error.
>
>
> *Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
> - 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
> (H82 - 2H8)*
>
> Is it really an issue or can I use -maxwarn?
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
-- 
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[gmx-users] Ligand simulation

[RAHUL SURESH]

for Command



*gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
I get the following error.


*Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
- 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
(H82 - 2H8)*

Is it really an issue or can I use -maxwarn?

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Ligand topology

[Mark Abraham]

Hi,

The run will be slightly slower with the restraints. But more significant
will be the further equilibration time to start to sample the unrestrained
ensemble.

Mark

On Thu, 30 Mar 2017 12:26 RAHUL SURESH  wrote:

> I am running NVT Equilibration for Protein_ligand complex as per the the
> tutorial.
>
> Will time consumption for equilibration increase in applying position
> restrains for both ligand and protein?
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Ligand topology

[RAHUL SURESH]

I am running NVT Equilibration for Protein_ligand complex as per the the
tutorial.

Will time consumption for equilibration increase in applying position
restrains for both ligand and protein?

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] Ligand-protein free binding energy is become positive

[masoud aliyar]

I’m using MM-PBSA on gromacs to calculate free binding energy of some
ligands into K-Ras (pdb-ID: 4epy). To validate MD simulation protocol and
to setup a rational threshold for evaluating the results, the co-crystal
ligand was considered as the reference ligand. Results showed that free
binding energy of reference ligand and my selected ligands have positive
quantities. Due to the fact that we are sure about the binding of reference
ligand into the binding pocket. How can we describe positive value of the
free binding energy? Results of MM-PBSA calculation for reference ligand is
as below:

Reference ligand:

van der Waal energy  =-166.208   +/-   32.482 kJ/mol

 Electrostattic energy= 144.473   +/-   15.430 kJ/mol

 Polar solvation energy   = 529.921   +/-   91.034 kJ/mol

 SASA energy  = -18.937   +/-3.458 kJ/mol

 SAV energy   =   0.000   +/-0.000 kJ/mol

 WCA energy   =   0.000   +/-0.000 kJ/mol

 Binding energy   = 489.143   +/-   46.438 kJ/mol
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Re: [gmx-users] Ligand hybridization

[Justin Lemkul]

On 7/6/16 12:26 PM, Chetan Puri wrote:

I am confused with the fact that after processing ligand through prodrg
whatever pdb file you get it doesn't show aromatic ring double bonds( if we
view it using pymol or vmd)
And I don't understand that although it shows aromatic ring planar but no
double bonds are present.
So is it the way aromatic ring is supposed to be after passing through
prodrg.


It has nothing to do with PRODRG (which hopefully you aren't using for 
topologies, unless you're manually correcting them) and everything to do with 
the visualization software.  Most programs don't explicitly render double bonds, 
anyway.


-Justin


On 5 Jul 2016 10:26 pm, "Justin Lemkul"  wrote:




On 7/5/16 10:50 AM, Chetan Puri wrote:


I am trying to do a protein- ligand simulation.

And the prodrg server provides the ligand out  put by completely removing
the double bonds(making it saturated)

So is there any way to do it.



See the PRODRG FAQ for dealing with incorrect protonation.  Then make sure
you fix the PRODRG topology because the charges won't be right.  Or use a
better server like ATB.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Ligand hybridization

[Chetan Puri]

I am confused with the fact that after processing ligand through prodrg
whatever pdb file you get it doesn't show aromatic ring double bonds( if we
view it using pymol or vmd)
And I don't understand that although it shows aromatic ring planar but no
double bonds are present.
So is it the way aromatic ring is supposed to be after passing through
prodrg.
On 5 Jul 2016 10:26 pm, "Justin Lemkul"  wrote:

>
>
> On 7/5/16 10:50 AM, Chetan Puri wrote:
>
>> I am trying to do a protein- ligand simulation.
>>
>> And the prodrg server provides the ligand out  put by completely removing
>> the double bonds(making it saturated)
>>
>> So is there any way to do it.
>>
>>
> See the PRODRG FAQ for dealing with incorrect protonation.  Then make sure
> you fix the PRODRG topology because the charges won't be right.  Or use a
> better server like ATB.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
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Re: [gmx-users] Ligand hybridization

[sun]

Use ATB for sure. PRODRG co-ordinates, charges are highly doubtful. I have 
prepared my ligand's topology using PRODRG and it took me almost 10 days to 
correct the charges. ATB is pretty good. 

Sent from my iPhone

> On 05-Jul-2016, at 10:26 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 7/5/16 10:50 AM, Chetan Puri wrote:
>> I am trying to do a protein- ligand simulation.
>> 
>> And the prodrg server provides the ligand out  put by completely removing
>> the double bonds(making it saturated)
>> 
>> So is there any way to do it.
> 
> See the PRODRG FAQ for dealing with incorrect protonation.  Then make sure 
> you fix the PRODRG topology because the charges won't be right.  Or use a 
> better server like ATB.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
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Re: [gmx-users] Ligand hybridization

[Justin Lemkul]

On 7/5/16 10:50 AM, Chetan Puri wrote:

I am trying to do a protein- ligand simulation.

And the prodrg server provides the ligand out  put by completely removing
the double bonds(making it saturated)

So is there any way to do it.



See the PRODRG FAQ for dealing with incorrect protonation.  Then make sure you 
fix the PRODRG topology because the charges won't be right.  Or use a better 
server like ATB.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] Ligand hybridization

[Chetan Puri]

I am trying to do a protein- ligand simulation.

And the prodrg server provides the ligand out  put by completely removing
the double bonds(making it saturated)

So is there any way to do it.
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Re: [gmx-users] Ligand breaks during energy minimization

[Soumya Lipsa Rath]

>> Dear Justin and Nikhil,
>>
>> Many thanks for your suggestions. Justin, I had optimized the parameters
>> using VMD's FFTK toolkit, so I just replaced my results in the *.str file
>> obtained from paramchem.
>>
>> I tried minimizing the ligand in vaccum and in a solvent box, in both
>> cases, the molecule just scatters apart (pardon me, the bond doesn't
>> break).
>>
>> I think there might be something wrong with the topology. However, I just
>> followed the general steps.
>>

>Well, when relying on automated methods fails, you have to roll your
sleeves up
>and do the work yourself :)
>
>If you can provide the stream file and coordinates of the ligand, I will
try to
>offer suggestions; if you can share them publicly across the list it may be
>informative for others to listen in on the conversation.
>
>Note, though, that the CGenFF paper is itself a tutorial on how to
parametrize
>small molecules, and there are even more detailed CGenFF tutorials
available
>online (check our website).
>
>-Justin

Dear Justin,

I could solve the problem finally! It was a stupid error where the input
str file had problems in the angle definition. Now, I rechecked each of the
steps and found the mistake.

Thank you once again for all your suggestions.

Soumya
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Re: [gmx-users] Ligand breaks during energy minimization

[Justin Lemkul]

On 3/25/16 8:03 PM, Soumya Lipsa Rath wrote:

Dear Justin and Nikhil,

Many thanks for your suggestions. Justin, I had optimized the parameters
using VMD's FFTK toolkit, so I just replaced my results in the *.str file
obtained from paramchem.

I tried minimizing the ligand in vaccum and in a solvent box, in both
cases, the molecule just scatters apart (pardon me, the bond doesn't
break).

I think there might be something wrong with the topology. However, I just
followed the general steps.



Well, when relying on automated methods fails, you have to roll your sleeves up 
and do the work yourself :)


If you can provide the stream file and coordinates of the ligand, I will try to 
offer suggestions; if you can share them publicly across the list it may be 
informative for others to listen in on the conversation.


Note, though, that the CGenFF paper is itself a tutorial on how to parametrize 
small molecules, and there are even more detailed CGenFF tutorials available 
online (check our website).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Ligand breaks during energy minimization

[Soumya Lipsa Rath]

Dear Justin and Nikhil,

Many thanks for your suggestions. Justin, I had optimized the parameters
using VMD's FFTK toolkit, so I just replaced my results in the *.str file
obtained from paramchem.

I tried minimizing the ligand in vaccum and in a solvent box, in both
cases, the molecule just scatters apart (pardon me, the bond doesn't
break).

I think there might be something wrong with the topology. However, I just
followed the general steps.

Thanks,
Soumya
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Re: [gmx-users] Ligand breaks during energy minimization

[Justin Lemkul]

On 3/25/16 9:33 AM, Nikhil Maroli wrote:

Dear justin,
if the topology is bad how bonds will break in MD? am i missing anything



The bonds don't break.  The OP was presumably using some imprecise language to 
describe a badly distorted structure.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Ligand breaks during energy minimization

[Nikhil Maroli]

Dear justin,
if the topology is bad how bonds will break in MD? am i missing anything

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Re: [gmx-users] Ligand breaks during energy minimization

[Justin Lemkul]

On 3/24/16 8:35 PM, Soumya Lipsa Rath wrote:

Dear gromacs users,

I have a protein-ligand system to simulate. I got the parameters from
CHARMM CGENFF and converted it to gromacs compatible parameters using
"cgenff_charmm2gmx.py" script as Justin had suggested previously.
Following the Protein-ligand tutorial of gromacs closely, I included the
lig.itp and lig.prm file in my original only protein topology file,
modified the output gro file making it a protein-ligand complex gro file.
After solvation and addition of ions, when I am trying to run an energy
minimization, my ligand breaks into pieces.

Could anyone please give insights on what I might be doing wrong?



Try to minimize the ligand in vacuo, and in a box of water.  If those produce a 
distorted structure, you have a suboptimal topology.  Note that the stream file 
from CGenFF lists all penalty values; large values mean your work is not done! 
If the ligand minimizes properly in vacuo and in water, then the problem is with 
your construction of the complex (e.g. changes in coordinates, etc).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Ligand breaks during energy minimization

[Nikhil Maroli]

Soumya Lipsa Rath  writes:

> 
> Dear gromacs users,
> 
> I have a protein-ligand system to simulate. I got the parameters from
> CHARMM CGENFF and converted it to gromacs compatible parameters using
> "cgenff_charmm2gmx.py" script as Justin had suggested previously.
> Following the Protein-ligand tutorial of gromacs closely, I included the
> lig.itp and lig.prm file in my original only protein topology file,
> modified the output gro file making it a protein-ligand complex gro 
file.
> After solvation and addition of ions, when I am trying to run an energy
> minimization, my ligand breaks into pieces.


There wont be any bond breaking or formation in MD,observe carefully.if 
your saying the ligand going apart from the protein-there are many methods 
to fix it ,
> 
> Could anyone please give insights on what I might be doing wrong?
> 
> Thanks,
> Soumya




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[gmx-users] Ligand breaks during energy minimization

[Soumya Lipsa Rath]

Dear gromacs users,

I have a protein-ligand system to simulate. I got the parameters from
CHARMM CGENFF and converted it to gromacs compatible parameters using
"cgenff_charmm2gmx.py" script as Justin had suggested previously.
Following the Protein-ligand tutorial of gromacs closely, I included the
lig.itp and lig.prm file in my original only protein topology file,
modified the output gro file making it a protein-ligand complex gro file.
After solvation and addition of ions, when I am trying to run an energy
minimization, my ligand breaks into pieces.

Could anyone please give insights on what I might be doing wrong?

Thanks,
Soumya
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[gmx-users] ligand topology & charge calculations

[Chetan Puri]

Can somebody suggest what could be the best possible way for generating
small molecules topology file and charge determination ( OPLS force field)
as I want carry out a simulation for miscell formation between small
ligands.
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[gmx-users] Ligand Virtual Sites

[Joan Clark Nicolas]

Dear GMX users,
I am trying to generate a custom virtual site for a C-NH3 group of a
ligand.
As a first test, I would like to use the parameters of the Lys virtual
site, but I can't see how the coordinates of the dummy atoms are generated
(I have already checked the tutorial and the gromacs manual). Can you help
me or redirect me to a paper/book where it is explained?

Thank you!
*Joan Clark i Nicolas*
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[gmx-users] ligand contact map

[Albert]

Hello:

I would like to calculate which residues does my ligand contact with 
during the MD simulation. I am just wondering is there any module for 
calculating ligand contact map?


Thank you very much

Albert
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Re: [gmx-users] ligand contact map

[Teemu Murtola]

Hi,

At least for some definitions of contacts, you can get what you want with
suitable use of gmx select. With a suitable selection that selects residues
that you consider to be in contact, and depending on what you want, -on,
-om, or -of should give you something useful.

Best regards,
Teemu

On Fri, Oct 16, 2015, 09:05 Albert  wrote:

> Hello:
>
> I would like to calculate which residues does my ligand contact with
> during the MD simulation. I am just wondering is there any module for
> calculating ligand contact map?
>
> Thank you very much
>
> Albert
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Re: [gmx-users] Ligand covalently bound to protein: Best practice

[Ebert Maximilian]

Thanks for your comment and sorry for my weird english. I must have been in my 
thoughts :).

I was also wondering if I attach covalently a protein to another protein or a 
large organic molecule through a residue in the middle of the sequence my 
approach would not work. Does anyone have a suggestion how setup a system like 
this?

Thanks,
Max


 On May 21, 2015, at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote:
 
 
 
 On 5/21/15 4:30 PM, Ebert Maximilian wrote:
 Hi there,
 
 I am about to setup a protein ligand complex in which the the amino acid is 
 covalently bound to the ligand. What I was about to do is to build an 
 artificial amino acid (in this case serine) with the ligand attached to it 
 an derive partial charges using antechamber or the RED server. Then while 
 preparing the force field in GROMACS I would treat the serine was a new 
 residue type with the new FF information. Is the a good practice?
 
 
 Sounds reasonable.
 
 -Justin
 
 -- 
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==
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Re: [gmx-users] Ligand covalently bound to protein: Best practice

[Justin Lemkul]

On 5/21/15 4:51 PM, Ebert Maximilian wrote:

Thanks for your comment and sorry for my weird english. I must have been in my 
thoughts :).

I was also wondering if I attach covalently a protein to another protein or a 
large organic molecule through a residue in the middle of the sequence my 
approach would not work. Does anyone have a suggestion how setup a system like 
this?



Why won't your approach work?  The answer to this question is always the same: a 
modified residue in a biopolymer requires a modified .rtp entry.  The details of 
how that works depends on the force field, but the net effect is the same.  For 
linking proteins, that's what specbond.dat is for.  The parametrization details 
depend on the kind of linkage.  Isopeptides, disulfides, etc. are already 
handled easily.  Other things require more effort.


-Justin


Thanks,
Max



On May 21, 2015, at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote:



On 5/21/15 4:30 PM, Ebert Maximilian wrote:

Hi there,

I am about to setup a protein ligand complex in which the the amino acid is 
covalently bound to the ligand. What I was about to do is to build an 
artificial amino acid (in this case serine) with the ligand attached to it an 
derive partial charges using antechamber or the RED server. Then while 
preparing the force field in GROMACS I would treat the serine was a new residue 
type with the new FF information. Is the a good practice?



Sounds reasonable.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] Ligand covalently bound to protein: Best practice

[Ebert Maximilian]

Hi there,

I am about to setup a protein ligand complex in which the the amino acid is 
covalently bound to the ligand. What I was about to do is to build an 
artificial amino acid (in this case serine) with the ligand attached to it an 
derive partial charges using antechamber or the RED server. Then while 
preparing the force field in GROMACS I would treat the serine was a new residue 
type with the new FF information. Is the a good practice? 

Thanks very much,

Max
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Re: [gmx-users] Ligand covalently bound to protein: Best practice

[Justin Lemkul]

On 5/21/15 4:30 PM, Ebert Maximilian wrote:

Hi there,

I am about to setup a protein ligand complex in which the the amino acid is 
covalently bound to the ligand. What I was about to do is to build an 
artificial amino acid (in this case serine) with the ligand attached to it an 
derive partial charges using antechamber or the RED server. Then while 
preparing the force field in GROMACS I would treat the serine was a new residue 
type with the new FF information. Is the a good practice?



Sounds reasonable.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Ligand Topology file

[neha bharti]

Hello All

I am performing Molecular dynamics simulation of protein and ligand
complex. I am using GROMOS96 53a6 force field. For Ligand topology file I
am using Automated topology builder.
In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o
ions.tpr) when I tried to add ion it gives me Note that

NOTE 2 [file topol.top]:
  The largest charge group contains 14 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


Following is the atom charge group of .itp file which I get from Automated
topology builder



[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1 C   16P5PC151   -0.050  12.0110
2 C   16P5PC1610.023  12.0110
3 C   16P5PC1710.023  12.0110
4 C   16P5PC181   -0.050  12.0110
5 C   16P5PC1910.023  12.0110
6 C   16P5PC2010.023  12.0110
7 C   16P5PC1410.580  12.0110
8 O   16P5P O1 1   -0.571  15.9994
9 C   16P5PC2110.570  12.0110
   10 O  16P5P O21   -0.571  15.9994  ;  0.000
   11 N  16P5P N32   -0.486  14.0067
   12 H  16P5PH1120.486   1.0080  ;  0.000
   13 C  16P5PC1230.251  12.0110
   14 C  16P5PC113   -0.019  12.0110
   15 C  16P5PC103   -0.070  12.0110
   16 C  16P5P C930.089  12.0110
   17 C  16P5P C83   -0.185  12.0110
   18 C  16P5PC133   -0.089  12.0110
   19 C  16P5P C730.491  12.0110
   20NR16P5P N23   -0.468  14.0067  ; -0.000
   21NR16P5P N14   -0.365  14.0067
   22 H  16P5P H140.365   1.0080  ;  0.000
   23 C  16P5P C550.155  12.0110
   24 C  16P5P C450.115  12.0110
   25 C  16P5P C65   -0.042  12.0110
   26 C  16P5P C35   -0.042  12.0110
   27 C  16P5P C25   -0.093  12.0110
   28 C  16P5P C15   -0.093  12.0110  ;  0.000
   29 N  16P5P N46   -0.486  14.0067
   30 H  16P5PH1660.486   1.0080  ;  0.000
   31 C  16P5PC2270.240  12.0110
   32 C  16P5PC277   -0.100  12.0110
   33 C  16P5PC267   -0.196  12.0110
   34 C  16P5PC2570.078  12.0110
   35 C  16P5PC247   -0.081  12.0110
   36 C  16P5PC237   -0.030  12.0110
   37 C  16P5PC2870.478  12.0110
   38NR16P5P N67   -0.475  14.0067
   39 C  16P5PC3470.138  12.0110
   40 C  16P5PC2970.170  12.0110
   41 C  16P5PC337   -0.030  12.0110
   42 C  16P5PC307   -0.030  12.0110
   43 C  16P5PC317   -0.081  12.0110
   44 C  16P5PC327   -0.081  12.0110  ;  0.000
   45NR16P5P N58   -0.365  14.0067
   46 H  16P5P H280.365   1.0080  ;  0.000
; total charge of the molecule:  -0.000



Should I ignore the error or is there something wrong in my charge group
generated from ATB.
Can any one please help me out to solve the problem.

Thanks You.

With Regards
Neha Bharti
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Re: [gmx-users] Ligand Topology file

[Justin Lemkul]

On 1/27/15 3:41 AM, neha bharti wrote:

Hello All

I am performing Molecular dynamics simulation of protein and ligand
complex. I am using GROMOS96 53a6 force field. For Ligand topology file I
am using Automated topology builder.
In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o
ions.tpr) when I tried to add ion it gives me Note that

NOTE 2 [file topol.top]:
   The largest charge group contains 14 atoms.
   Since atoms only see each other when the centers of geometry of the charge
   groups they belong to are within the cut-off distance, too large charge
   groups can lead to serious cut-off artifacts.
   For efficiency and accuracy, charge group should consist of a few atoms.
   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


Following is the atom charge group of .itp file which I get from Automated
topology builder



[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
 1 C   16P5PC151   -0.050  12.0110
 2 C   16P5PC1610.023  12.0110
 3 C   16P5PC1710.023  12.0110
 4 C   16P5PC181   -0.050  12.0110
 5 C   16P5PC1910.023  12.0110
 6 C   16P5PC2010.023  12.0110
 7 C   16P5PC1410.580  12.0110
 8 O   16P5P O1 1   -0.571  15.9994
 9 C   16P5PC2110.570  12.0110
10 O  16P5P O21   -0.571  15.9994  ;  0.000
11 N  16P5P N32   -0.486  14.0067
12 H  16P5PH1120.486   1.0080  ;  0.000
13 C  16P5PC1230.251  12.0110
14 C  16P5PC113   -0.019  12.0110
15 C  16P5PC103   -0.070  12.0110
16 C  16P5P C930.089  12.0110
17 C  16P5P C83   -0.185  12.0110
18 C  16P5PC133   -0.089  12.0110
19 C  16P5P C730.491  12.0110
20NR16P5P N23   -0.468  14.0067  ; -0.000
21NR16P5P N14   -0.365  14.0067
22 H  16P5P H140.365   1.0080  ;  0.000
23 C  16P5P C550.155  12.0110
24 C  16P5P C450.115  12.0110
25 C  16P5P C65   -0.042  12.0110
26 C  16P5P C35   -0.042  12.0110
27 C  16P5P C25   -0.093  12.0110
28 C  16P5P C15   -0.093  12.0110  ;  0.000
29 N  16P5P N46   -0.486  14.0067
30 H  16P5PH1660.486   1.0080  ;  0.000
31 C  16P5PC2270.240  12.0110
32 C  16P5PC277   -0.100  12.0110
33 C  16P5PC267   -0.196  12.0110
34 C  16P5PC2570.078  12.0110
35 C  16P5PC247   -0.081  12.0110
36 C  16P5PC237   -0.030  12.0110
37 C  16P5PC2870.478  12.0110
38NR16P5P N67   -0.475  14.0067
39 C  16P5PC3470.138  12.0110
40 C  16P5PC2970.170  12.0110
41 C  16P5PC337   -0.030  12.0110
42 C  16P5PC307   -0.030  12.0110
43 C  16P5PC317   -0.081  12.0110
44 C  16P5PC327   -0.081  12.0110  ;  0.000
45NR16P5P N58   -0.365  14.0067
46 H  16P5P H280.365   1.0080  ;  0.000
; total charge of the molecule:  -0.000



Should I ignore the error or is there something wrong in my charge group
generated from ATB.
Can any one please help me out to solve the problem.



There are several charge groups that are too large, and group 7 is the one that 
is triggering the problem.  Note that charge groups are only relevant for the 
group cutoff scheme, and are ignored with Verlet.  Scrutinize all elements of 
the topology; if something as fundamental as the charge groups (which should 
only ever encompass 2-4 atoms based on chemical moiety) are this bizarre, likely 
the charges are suboptimal, as well.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--

[gmx-users] ligand related problem

[RINU KHATTRI]

hello gromacs users
i am working on complex with popc membrane
i am facing the problem -- ligand is not attached in the protein
i am following the previous mail protocol
and pasted the ligand in final system_shrink.gro file after this i saw
the .gro file in vmd ligand is very distant to protein it is not
attached with the protein
kindly help

 pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc

grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact

editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.41840
6.44350 6.59650

cat KALP_newbox.gro dppc128_whole.gro  system.gro

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat



grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr

 mdrun -v -deffnm em

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
28 iteration
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Re: [gmx-users] ligand related problem

[Justin Lemkul]

On 12/2/14 6:00 AM, RINU KHATTRI wrote:

hello gromacs users
i am working on complex with popc membrane
i am facing the problem -- ligand is not attached in the protein
i am following the previous mail protocol
and pasted the ligand in final system_shrink.gro file after this i saw
the .gro file in vmd ligand is very distant to protein it is not


The list does not accept attachments.  If you want to share a file or image, 
post it to a file-sharing service and provide the URL in your email.



attached with the protein
kindly help

  pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc

grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact

editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.41840
6.44350 6.59650

cat KALP_newbox.gro dppc128_whole.gro  system.gro

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat



grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr

  mdrun -v -deffnm em

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
28 iteration



These commands are just copied and pasted directly from my tutorial; these are 
not what you should be using for any arbitrary system.  The logic is the same, 
but the actual commands must be tailored to your system.


Old versions of InflateGRO, IIRC, deleted ligands, so you had to place the 
protein-ligand complex in the proper box (to get the correct translated 
coordinates), remove the ligand, build, and paste the ligand back in.  Perhaps 
that is not the case any more and you can keep the entire protein-ligand complex 
intact throughout the whole process.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Ligand interaction

[md kashif]

Dear all
The protein+ligand complex energy is -1.05e+06  and energy of protein
only(without docking) is -1.5...e+06, what does it mean?

On Wed, Nov 12, 2014 at 9:57 AM, md kashif kashifzamir180...@gmail.com
wrote:

 Hello everyone
 please suggest me that is there any change in protein energy after docking
 the ligand to my energy minimized protein? my protein energy is
 -1.5e+06 and now after docking with ligand it becomes -1.05e+06.
 what does it mean?


 Thanks

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Re: [gmx-users] Ligand interaction

[Justin Lemkul]

On 11/12/14 5:10 AM, md kashif wrote:

Dear all
The protein+ligand complex energy is -1.05e+06  and energy of protein
only(without docking) is -1.5...e+06, what does it mean?



It means that you have two systems with two different energies.  In order to 
dock the ligand, you must have started from a protein without water.  In 
solvating the system afterwards, you ended up with a different number of solvent 
molecules (because there is now less void space in the protein's binding site) 
and therefore the energy surface during minimization is different.  You're 
comparing apples to oranges.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Ligand is not in the same position as in PDB file

[neha bharti]

Hello All

I am trying to perform MD for protein-ligand complex in popc lipid with
charmm36 force field and also follow Justin A. Lemkul tutorial.
I downloaded the pdb structure of protein and ligand complex and the
separate the protein and ligand file and prepare the system.

Finally I perform the MD run for 100 ns, I found that the ligand is not in
the same place as present in PDB file of protein ligand complex.

Is it necessary that the protein should be in the same position as present
in protein ligand complex PDB file ??

Is there something wrong in my work.

Please Help.

Thanks and regards

Neha Bharty
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Re: [gmx-users] Ligand is not in the same position as in PDB file

[Mark Abraham]

Hi,

Probably you are seeing normal behaviour in the presence of
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
If you want to visualize the protein and ligand as a complex, you need to
post-process the output accordingly. mdrun doesn't know that you plan to
treat them as special.

Mark

On Tue, Nov 11, 2014 at 9:50 AM, neha bharti nehabharty...@gmail.com
wrote:

 Hello All

 I am trying to perform MD for protein-ligand complex in popc lipid with
 charmm36 force field and also follow Justin A. Lemkul tutorial.
 I downloaded the pdb structure of protein and ligand complex and the
 separate the protein and ligand file and prepare the system.

 Finally I perform the MD run for 100 ns, I found that the ligand is not in
 the same place as present in PDB file of protein ligand complex.

 Is it necessary that the protein should be in the same position as present
 in protein ligand complex PDB file ??

 Is there something wrong in my work.

 Please Help.

 Thanks and regards

 Neha Bharty
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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Re: [gmx-users] Ligand is not in the same position as in PDB file

[neha bharti]

Thank you very much mark for your reply.
I merge the protein and ligand file before starting the molecular dynamics
simulation.
Then I start the MD run.
I don't how to  post-process the output. can you please tell me how to
perform it or is there any article or tutorial available for that.

Thanks and regards
Neha Bharty


Hi,

Probably you are seeing normal behaviour in the presence of
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
.
If you want to visualize the protein and ligand as a complex, you need to
post-process the output accordingly. mdrun doesn't know that you plan to
treat them as special.

Mark

On Tue, Nov 11, 2014 at 9:50 AM, neha bharti nehabharty...@gmail.com
wrote:

 Hello All

 I am trying to perform MD for protein-ligand complex in popc lipid with
 charmm36 force field and also follow Justin A. Lemkul tutorial.
 I downloaded the pdb structure of protein and ligand complex and the
 separate the protein and ligand file and prepare the system.

 Finally I perform the MD run for 100 ns, I found that the ligand is not
in
 the same place as present in PDB file of protein ligand complex.

 Is it necessary that the protein should be in the same position as
present
 in protein ligand complex PDB file ??

 Is there something wrong in my work.

 Please Help.

Thanks and regard
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Re: [gmx-users] Ligand is not in the same position as in PDB file

[Mark Abraham]

Hi,

Did you consult the link I provided? ;-)

Mark

On Tue, Nov 11, 2014 at 11:18 AM, neha bharti nehabharty...@gmail.com
wrote:

 Thank you very much mark for your reply.
 I merge the protein and ligand file before starting the molecular dynamics
 simulation.
 Then I start the MD run.
 I don't how to  post-process the output. can you please tell me how to
 perform it or is there any article or tutorial available for that.

 Thanks and regards
 Neha Bharty


 Hi,

 Probably you are seeing normal behaviour in the presence of
 
 http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
 
 http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
 
 .
 If you want to visualize the protein and ligand as a complex, you need to
 post-process the output accordingly. mdrun doesn't know that you plan to
 treat them as special.

 Mark

 On Tue, Nov 11, 2014 at 9:50 AM, neha bharti nehabharty...@gmail.com
 wrote:

  Hello All
 
  I am trying to perform MD for protein-ligand complex in popc lipid with
  charmm36 force field and also follow Justin A. Lemkul tutorial.
  I downloaded the pdb structure of protein and ligand complex and the
  separate the protein and ligand file and prepare the system.
 
  Finally I perform the MD run for 100 ns, I found that the ligand is not
 in
  the same place as present in PDB file of protein ligand complex.
 
  Is it necessary that the protein should be in the same position as
 present
  in protein ligand complex PDB file ??
 
  Is there something wrong in my work.
 
  Please Help.
 
 Thanks and regard
 --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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