Re: [gmx-users] (no subject)

[Tasneem Kausar]

Number of hydrogen bond depends on the nature of your drug. It can be zero,
one or many.

On Thu, Aug 10, 2017 at 10:33 AM, saranya  wrote:

> Hi,
> I have done protein-drug simulations for 100ns. While calculating the
> hydrogen bond between the protein-drug complex I am getting only 2 hydrogen
> bonds.
> I just want to clarify that 2 hydrogen bonds mean very low, is it
> acceptable to get this minimum number of bond formation for the protein
> drug interaction?
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
> --
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[gmx-users] (no subject)

[saranya]

Hi,
I have done protein-drug simulations for 100ns. While calculating the
hydrogen bond between the protein-drug complex I am getting only 2 hydrogen
bonds.
I just want to clarify that 2 hydrogen bonds mean very low, is it
acceptable to get this minimum number of bond formation for the protein
drug interaction?

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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[gmx-users] (no subject)

[saranya]

Hi,
I have done protein-drug simulations for 100ns. While calculating the
hydrogen bond between the protein-drug complex I am getting only 2 hydrogen
bonds.
I just want to clarify that 2 hydrogen bonds mean very low, is it
acceptable to get this minimum number of bond formation for the protein
drug interaction?

With Regards,

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*

*Coimbatore-46*
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[gmx-users] gmx sasa

[Mohammad Zahidul Hossain Khan]

Dear Sir

Does anyone know how to measure the SASA energy with unit (kj/mol or
kcal/mol)

when i give this command:
*gmx sasa -f b.trr -s b.tpr -o b.xvg*
I got in Y-axix "Area (nm\S2\N)"

and when I give this command
*gmx sasa -f b.trr -s b.tpr -odg b.xvg*
I got in Y axix "D Gsolv"
but I do not know the unit.
-- 


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

[Justin Lemkul]

On 8/9/17 1:31 PM, abhisek Mondal wrote:

Hi,

 I have a predicted secondary structure of a transmembrane protein
containing a really long alpha helix. If I place the secondary structure of
the protein inside membrane (as done for KALP in tutorial) and following
all the steps perform a production MD, is it possible to obtain a
thermodynamically favorable tertiary structure of the same protein ? I mean
generating the folds based on the membrane environment provided.



I'd be very skeptical.  Simulations can reasonably fold small motifs, but it 
requires a significant time scale and/or enhanced sampling approaches that may 
or may not be compatible with membranes.  Folding something large in such a 
medium (slowly diffusing lipids) will require extensive simulations as well as a 
very accurate force field.  I'm not sure if anyone has been able to make such an 
assessment in the literature yet.  What you're proposing is a very tall task, 
and potentially huge time investment for little or no useful data.


-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] (no subject)

[Alex]

I think it is all pretty simple, at least from what you are describe. If
there are sufficient reason to believe that your membrane should be flat
and not jagged, and your box size (supercell size, in the terminology you
probably prefer) is properly set up, simply allow it to relax in vacuum at
a very low temperature. Say, 5-10K? This is prior to solvating, etc.
I've never worked with MnO2, so I just can't say anything more specific,
sorry.

I hope this helps.

Alex

On Wed, Aug 9, 2017 at 12:10 PM, gangotri dey  wrote:

> Dear Alex and Mark,
>
> Thank you for your kind reply.
>
> To begin with I am a Postdoc but with expertise is in DFT. It is my first
> venture into force field MD calculations. Hence, I am struggling. My group
> and the boss has similar expertise. So we have turned to public forums to
> ask questions.
>
> My system is a brick floating in the water as you have correctly
> identified.
> My system is a periodic MnO2 surface. It has triclinic crystal system. I
> want it to be solvated in all 3 directions but within the boundary of the
> unit cell. This means that I do not want any water molecule between the
> surface and its continuous periodic image. I want the water to be maximum
> in the z-direction. I am using the 5.0.4 version. I tried gmx_mpi
> insert_molecule and then -nmol and -ip option. But this still generates a
> structure with water molecules beyond the desired x and y plane. I am not
> sure how can I get this done as desired.
>
> If the question and the problem are not very clear, please let me know. I
> will try to reframe my words.
>
> Looking forward to a healthy discussion.
>
> Thank you
> G.
>
>
>
>
> *Thank you*
>
> *Gangotri Dey*
> Postdoctoral Associate
> Rutgers University New Brunswick
> Chemistry and Chemical Biology
> 174 Frelinghuysen Road, Piscataway, NJ 08854
> Phone: +16092162254
>
>
>
>
> On Mon, Aug 7, 2017 at 8:06 PM, Alex  wrote:
>
> >
> > I did not quite understand your comment.
> >>>
> >>> However, I am trying my best to answer it.
> >>> I have a surface MnO2 model. I have solvated the structure in all 3
> >>> directions. After that, I minimize it and run NVT simulation with the
> >>> parameters as mentioned. However, I see that there is a deformation of
> >>> the
> >>> surface and it does not remain a flat surface. Instead, it curls like a
> >>> ribbon. This should not be the case. Hence, I am wondering what are the
> >>> factors that can lead to this deformation? Are the parameters in the
> NVT
> >>> simulation good enough or else there is a problem that I cannot see.
> >>>
> >>> G
> >>>
> >>> There are a few points to be made...
> > 1. The shape of your system, which is "solvated in all 3 directions" is
> > very unclear. Is this a brick floating in water?
> > 2. Please do not solvate anything until you have established that your
> > "surface" is happy in vacuum.
> > 3. If you have bending as a whole, it could be indicative of large
> > internal strains, in which case NVT is probably a poor option. When you
> say
> > you have "a surface MnO2 model," is it something like this?
> > https://upload.wikimedia.org/wikipedia/commons/8/81/Manganes
> > e-dioxide-from-xtal-sheet-3D-balls.png
> > 4. This community is mostly focused on biomolecular simulations and noone
> > will be able to verify your parameterization of a solid crystal. Here is
> > the rule of thumb though: If something bends when it shouldn't bend, your
> > model is bad, which really has nothing to do with Gromacs.
> > 5. If you are a student and points 1-4 aren't something your doctoral
> > advisor already mentioned, maybe you should find another advisor.
> >
> > Alex
> >
> >
> > Hi,
> 
>  Are you trying to implement a model that you know is capable of
> produce
>  a
>  surface that does not deform in unexpected ways?
> 
>  Mark
> 
>  On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:
> 
>  Dear all,
> >
> > I am trying to equilibrate a MnO2 surface (not cluster but
> periodic). I
> > have solvated the surface with water in all 3 directions. After the
> NVT
> > run, I see that the surface is deformed. I was wondering what else
> can
> >
>  I
> >>>
>  add in my nvt.mdp to not encounter this problem?
> >
> > I have mainly followed the examples in the forum for graphene/CNT
> >
>  growth.
> >>>
>  title   = MnO2  in H2O NVT equilibration
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 5 ; 2 * 50 = 100 ps
> > dt  = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 50; save coordinates every 0.10 ps
> > nstvout = 50; save velocities every 0.10 ps
> > nstenergy   = 50; save energies every 0.10 ps
> > nstlog  = 50; update log file every 0.10 ps
> 

Re: [gmx-users] (no subject)

[gangotri dey]

Dear Alex and Mark,

Thank you for your kind reply.

To begin with I am a Postdoc but with expertise is in DFT. It is my first
venture into force field MD calculations. Hence, I am struggling. My group
and the boss has similar expertise. So we have turned to public forums to
ask questions.

My system is a brick floating in the water as you have correctly
identified.
My system is a periodic MnO2 surface. It has triclinic crystal system. I
want it to be solvated in all 3 directions but within the boundary of the
unit cell. This means that I do not want any water molecule between the
surface and its continuous periodic image. I want the water to be maximum
in the z-direction. I am using the 5.0.4 version. I tried gmx_mpi
insert_molecule and then -nmol and -ip option. But this still generates a
structure with water molecules beyond the desired x and y plane. I am not
sure how can I get this done as desired.

If the question and the problem are not very clear, please let me know. I
will try to reframe my words.

Looking forward to a healthy discussion.

Thank you
G.




*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Mon, Aug 7, 2017 at 8:06 PM, Alex  wrote:

>
> I did not quite understand your comment.
>>>
>>> However, I am trying my best to answer it.
>>> I have a surface MnO2 model. I have solvated the structure in all 3
>>> directions. After that, I minimize it and run NVT simulation with the
>>> parameters as mentioned. However, I see that there is a deformation of
>>> the
>>> surface and it does not remain a flat surface. Instead, it curls like a
>>> ribbon. This should not be the case. Hence, I am wondering what are the
>>> factors that can lead to this deformation? Are the parameters in the NVT
>>> simulation good enough or else there is a problem that I cannot see.
>>>
>>> G
>>>
>>> There are a few points to be made...
> 1. The shape of your system, which is "solvated in all 3 directions" is
> very unclear. Is this a brick floating in water?
> 2. Please do not solvate anything until you have established that your
> "surface" is happy in vacuum.
> 3. If you have bending as a whole, it could be indicative of large
> internal strains, in which case NVT is probably a poor option. When you say
> you have "a surface MnO2 model," is it something like this?
> https://upload.wikimedia.org/wikipedia/commons/8/81/Manganes
> e-dioxide-from-xtal-sheet-3D-balls.png
> 4. This community is mostly focused on biomolecular simulations and noone
> will be able to verify your parameterization of a solid crystal. Here is
> the rule of thumb though: If something bends when it shouldn't bend, your
> model is bad, which really has nothing to do with Gromacs.
> 5. If you are a student and points 1-4 aren't something your doctoral
> advisor already mentioned, maybe you should find another advisor.
>
> Alex
>
>
> Hi,

 Are you trying to implement a model that you know is capable of produce
 a
 surface that does not deform in unexpected ways?

 Mark

 On Mon, 7 Aug 2017 16:35 gangotri dey  wrote:

 Dear all,
>
> I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
> have solvated the surface with water in all 3 directions. After the NVT
> run, I see that the surface is deformed. I was wondering what else can
>
 I
>>>
 add in my nvt.mdp to not encounter this problem?
>
> I have mainly followed the examples in the forum for graphene/CNT
>
 growth.
>>>
 title   = MnO2  in H2O NVT equilibration
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 50 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 50; save coordinates every 0.10 ps
> nstvout = 50; save velocities every 0.10 ps
> nstenergy   = 50; save energies every 0.10 ps
> nstlog  = 50; update log file every 0.10 ps
> ; Bond parameters
> continuation= no; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = none  ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 10; 20 fs, largely irrelevant
>
 with
>>>
 Verlet
> rcoulomb= 1.0   ; short-range electrostatic
>
 cutoff

> (in nm)
> rvdw  

[gmx-users] transmembrane protein simulation

[abhisek Mondal]

Hi,

I have a predicted secondary structure of a transmembrane protein
containing a really long alpha helix. If I place the secondary structure of
the protein inside membrane (as done for KALP in tutorial) and following
all the steps perform a production MD, is it possible to obtain a
thermodynamically favorable tertiary structure of the same protein ? I mean
generating the folds based on the membrane environment provided.

   Being a beginner in membrane protein simulation, any given advice 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*
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Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation

[Maghesree Chakraborty]

Hello,

Thanks for your reply.

Regards,
M. Chakraborty

On Mon, Aug 7, 2017 at 4:56 PM, Mark Abraham 
wrote:

> Hi,
>
> Ok, I didn't understand you because I didn't have enough information yet.
> IIRC your topology will still have to specify the constraint bond length,
> you can't have grompp infer it from the starting coordinates. You should
> also get a single molecule working correctly, because the symptoms of
> broken topology and broken initial coordinates are often not
> distinguishable. Prove the topology first when there cannot be an
> inter-molecular clash.
>
> Mark
>
> On Mon, 7 Aug 2017 22:00 Maghesree Chakraborty 
> wrote:
>
> > Thank you for your response. I did not have tabulated potentials for
> bonded
> > interactions. I had tabulated potentials only for non-bonded
> > interactions. I had set constraints to be all-angles in my mdp file. I
> will
> > try using "constraint" interaction explicitly in my topology instead of
> > converting bonds and angles into constraints via mdp directive.
> >
> > On Mon, Aug 7, 2017 at 1:58 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Tabulated bonded interactions are the opposite of constraints. You can
> > > explicitly use a "constraint" interaction type in your topology, which
> > > sounds like a good start. See chapter five of the reference manual.
> > >
> > > Mark
> > >
> > > On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty 
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > I am trying to run a CG simulation with only non-bonded
> interactions. I
> > > > have obtained the tabulated potentials for those interactions by
> > > > force-matching using VOTCA. I want all my bonds and angles to be
> > > > constrained as they are in the initial cg_conf.gro file. Since I do
> not
> > > > have tabulated potentials for bonded interactions, gromacs gives
> error
> > > if I
> > > > do not provide the bond and angle parameters (b0,kb and θ0 , kθ) in
> the
> > > > topology file. Then I tried setting the bond parameter (b0) to be the
> > > mean
> > > > of bond-length distribution in cg_conf.gro and the angle parameter
> (θ0)
> > > to
> > > > be the mean of the angle distribution in cg_conf.gro, I constrain the
> > > bonds
> > > > and angles with LINCS in my grompp file. During simulation, I get a
> lot
> > > of
> > > > LINCS warning and simulation is aborted. I am wondering if there is a
> > way
> > > > of constraining the initial configurations of the molecules as they
> are
> > > in
> > > > cg_conf.gro file  in the absence of tabulated bonded potentials and
> not
> > > > forcing the molecules to have the bond-lengths and angles as
> specified
> > > by
> > > > the topology parameters.
> > > >
> > > > Thank you.
> > > >
> > > > Regards,
> > > > M. Chakraborty
> > > > --
> > > > Gromacs Users mailing list
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Re: [gmx-users] remove the jumps over the boundaries

[farial tavakoli]

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


Sent from Yahoo Mail for iPhone


On Wednesday, August 9, 2017, 5:36 PM, Milan Melichercik 
 wrote:

‎Hi,
The message says you have used older Gromacs for analysis than was the tpr file 
was created with. For 2016.x versions you have to use "gmx trjconv" instead of 
plain trjconv. The trjconv you have called is probably from your Linux 
distribution and in old version - you can find its binary file using "which 
trjconv"‎.
BTW why do you store the output to odb file? Cause it will be huge. You should 
extract only one frame (starting/final) using -dump and than the whole 
trajectory to xtc file (sure you can use -dt switch or you can skip frames in 
VMD during the load of xtc file).

Best,

Milan

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: ‪farial tavakoli‬ ‪
Sent: streda, 9. augusta 2017 14:18
To: Discussion List for GROMACS Users
Reply To: gmx-us...@gromacs.org
Subject: [gmx-users] remove the jumps over the boundaries

Dear GROMACS users
I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to 
visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD 
, it has pbc problem, so I issued this command:
trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10
but faced to this error:
Fatal error:
reading tpx file (md_0_1.tpr) version 110 with version 83 program

is anybody help me to solve this problem?
thanks in advanceFarial
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Re: [gmx-users] g_cluster and g_hbond calculation on GPU

[Mark Abraham]

Hi,

Please don't re-post the same questions from different emails. You already
got the answer that no analysis tools have been ported to run on GPUs.

Mark

On Wed, Aug 9, 2017 at 3:04 PM Kishwar Hayat Khan 
wrote:

> Hi Everyone,
> I would like to run g_cluster and g_hbond calculation on GPU boards. I
> could only find -nthreads option to fasten my calculations, Is it possible
> to use GPU boards for this like mdrun.
> reg
> Kish
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Re: [gmx-users] remove the jumps over the boundaries

[Milan Melichercik]

‎Hi,
The message says you have used older Gromacs for analysis than was the tpr file 
was created with. For 2016.x versions you have to use "gmx trjconv" instead of 
plain trjconv. The trjconv you have called is probably from your Linux 
distribution and in old version - you can find its binary file using "which 
trjconv"‎.
BTW why do you store the output to odb file? Cause it will be huge. You should 
extract only one frame (starting/final) using -dump and than the whole 
trajectory to xtc file (sure you can use -dt switch or you can skip frames in 
VMD during the load of xtc file).

Best,

Milan

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: ‪farial tavakoli‬ ‪
Sent: streda, 9. augusta 2017 14:18
To: Discussion List for GROMACS Users
Reply To: gmx-us...@gromacs.org
Subject: [gmx-users] remove the jumps over the boundaries

Dear GROMACS users
I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to 
visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD 
, it has pbc problem, so I issued this command:
trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10
but faced to this error:
Fatal error:
reading tpx file (md_0_1.tpr) version 110 with version 83 program

is anybody help me to solve this problem?
thanks in advanceFarial
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[gmx-users] g_cluster and g_hbond calculation on GPU

[Kishwar Hayat Khan]

Hi Everyone,
I would like to run g_cluster and g_hbond calculation on GPU boards. I
could only find -nthreads option to fasten my calculations, Is it possible
to use GPU boards for this like mdrun.
reg
Kish
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Re: [gmx-users] Atom OXT in residue was not found

[Qinghua Liao]

Dear Justin,

Thanks very much for your suggestion, it works well now.

All the best,
Qinghua

On 08/09/2017 01:28 PM, Justin Lemkul wrote:



On 8/9/17 7:21 AM, Qinghua Liao wrote:

Hello,

I want to simulate a protein with a ligand (small molecule, 15 
atoms). But I have problem of generating the topology file.
I added the topology of the ligand as a new residue in force field 
database (aminoacid.rtp), but I got the error when I run pdb2gmx

interactively with -ter and chose none for the ligand:

Atom OXT in residue DH2 495 was not found in rtp entry DH2 with 15 atoms

The problem is that there isn't any atom named OXT in the ligand. I 
also searched the mailing list, someone mentioned that
pdb2gmx might rename the atom name of the atoms in the ligand. I 
don't understand why pdb2gmx complains something like this

when the atom is not in the ligand. Any suggestions? Thanks a lot!



pdb2gmx is trying to apply C-terminal protein patching to your 
ligand.  If you have listed DH2 in residuetypes.dat as Protein, 
don't.  Also note that atom names are translated via xlateat.dat so if 
you have one of those atom names, and DH2 is considered a protein 
residue, you need to choose a different atom name.


-Justin



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Re: [gmx-users] g_hbonds calculation on GPU

[Erik Marklund]

Dear Rraj,

Nope. No-one has made GPU support for gmx hbond (or any other analysis tool as 
far as I know).

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 9 Aug 2017, at 14:16, Rituraj Purohit 
> wrote:

Hi Everyone,
I would like to run g_hbons calculation on GPU boards. I could only find
--nthreads option to fasten my calculations, Is it possible to use GPU
boards for this like mdrun.
reg
Rraj
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[gmx-users] remove the jumps over the boundaries

[‪farial tavakoli‬ ‪]

Dear GROMACS users
I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to 
visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD 
, it has pbc problem, so I issued this command:
trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10
but faced to this error:
Fatal error:
reading tpx file (md_0_1.tpr) version 110 with version 83 program

is anybody help me to solve this problem?
thanks in advanceFarial
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[gmx-users] g_hbonds calculation on GPU

[Rituraj Purohit]

Hi Everyone,
I would like to run g_hbons calculation on GPU boards. I could only find
--nthreads option to fasten my calculations, Is it possible to use GPU
boards for this like mdrun.
reg
Rraj
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Re: [gmx-users] Atom OXT in residue was not found

[Justin Lemkul]

On 8/9/17 7:21 AM, Qinghua Liao wrote:

Hello,

I want to simulate a protein with a ligand (small molecule, 15 atoms). But I 
have problem of generating the topology file.
I added the topology of the ligand as a new residue in force field database 
(aminoacid.rtp), but I got the error when I run pdb2gmx

interactively with -ter and chose none for the ligand:

Atom OXT in residue DH2 495 was not found in rtp entry DH2 with 15 atoms

The problem is that there isn't any atom named OXT in the ligand. I also 
searched the mailing list, someone mentioned that
pdb2gmx might rename the atom name of the atoms in the ligand. I don't 
understand why pdb2gmx complains something like this

when the atom is not in the ligand. Any suggestions? Thanks a lot!



pdb2gmx is trying to apply C-terminal protein patching to your ligand.  If you 
have listed DH2 in residuetypes.dat as Protein, don't.  Also note that atom 
names are translated via xlateat.dat so if you have one of those atom names, and 
DH2 is considered a protein residue, you need to choose a different atom name.


-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] Position restrains during alchemical transformation

[Mark Abraham]

Hi,

I presume the position-restraints file was written by a tool that didn't
anticipate this use case (and pdb2gmx likely does not). If so, I would edit
my position restraints file to express my intent, ie copy the functype and
parameters so that there's an A and B state on the same line, just as with
other topology pieces.

One could also use grompp -maxwarn, but laziness leads to hate, and hate
leads to the Dark Side. You will one day curse Past Hermann, because a
warning you ignored costs you months of wasted simulation time.

Mark

On Wed, Aug 9, 2017 at 11:27 AM Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Dear all,
>
> I have a questions concerning MD free energy calculations using
> alchemical tranformation. I want to restrain the backbone of my protein
> which I mutate during TI. However, I do not know how to correctly
> generate position restrains. If I use the position restrain file, which
> I generated for the A state, following warning shows up:
>
> WARNING 1 [file posre.itp, line 1470]:
>Some parameters for bonded interaction involving perturbed atoms are
>specified explicitly in state A, but not B - copying A to B
>
> Can I ignore this warning, or do you have any suggestions for me?
>
> All the best and thank you very much in advance
>
> Johannes
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[gmx-users] Position restrains during alchemical transformation

[Hermann, Johannes]

Dear all,

I have a questions concerning MD free energy calculations using 
alchemical tranformation. I want to restrain the backbone of my protein 
which I mutate during TI. However, I do not know how to correctly 
generate position restrains. If I use the position restrain file, which 
I generated for the A state, following warning shows up:


WARNING 1 [file posre.itp, line 1470]:
  Some parameters for bonded interaction involving perturbed atoms are
  specified explicitly in state A, but not B - copying A to B

Can I ignore this warning, or do you have any suggestions for me?

All the best and thank you very much in advance

Johannes
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Re: [gmx-users] clayff forcefield

[Mark Abraham]

Hi,

Use gmx x2top -ff clayff, not gmx x2top -ff clayff.ff

Mark

On Wed, Aug 9, 2017 at 8:53 AM G R  wrote:

> On Wed, Aug 9, 2017 at 1:04 AM, <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
>
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users@maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
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> > or, via email, send a message with subject or body 'help' to
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. Re: clayff forcefield (Justin Lemkul)
> >2. (no subject) (Sorour Hasani)
> >3. Re: Generating topology file for a long polymer chain (Mahsa E)
> >4. convert .tpr to include energy groups (Tushar Ranjan Moharana)
> >5. Problem with Ryzen, threads and core dumps? (Steffen Graether)
> >
> >
> > --
> >
> > Message: 1
> > Date: Tue, 8 Aug 2017 08:37:34 -0400
> > From: Justin Lemkul 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] clayff forcefield
> > Message-ID: <73598616-91d0-a438-e92c-278cd2ee9...@vt.edu>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> >
> > Please don't reply to the entire digest; cut out only the relevant parts.
> >
> > On 8/8/17 2:37 AM, G R wrote:
> >
> > >>Hi,
> > >>
> > >   Thank you for your answer. yes, I know that I should make my own
> > > forcefield in my working directory, and I made this forcefield, but
> when
> > I
> > > use x2top to generate itp file, gromacs could not find  my own
> forcefield
> > > (I named the forcefield file clayff.ff) in my working directory.
> Gromacs
> > > use the oplsaa in the share/top file instead, and obviusly the itp file
> > > doesn't generate. So, I asked again to be sure about my procedure.
> > >
> > > In my last project I modified oplsaa for generating itp file for
> graphen
> > > and I did not have this problem. Gromacs could easily recognize the
> > > forcefiled file in current directory, but in clayff case I can't
> > understand
> > > why it read forcefield in shar/top instead of in current directory!
> > >
> > Probably because you're not selecting your force field properly.  gmx
> > x2top has
> > a -ff command-line argument, which defaults to OPLS-AA unless you specify
> > otherwise.  You haven't provided your actual command yet, but I suspect
> > that's
> > you're problem.
> >
> > -Justin
> >
> > Thank you Justin. I used this command gmx x2top -f conf.gro -o sys.itp
> -ff
> > clayff.ff. the error was ''couldn't find forcefield''. Then I used ''gmx
> > x2top -f con.gro -o sys.itp -ff select'' for interactive selection, and I
> > choosed clayff.ff. This time gromacs read the clayff forcefield in
> current
> > directory. Is it right to use select? or I should do something else?
> >
>
> > --
> >
> >
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Re: [gmx-users] convert .tpr to include energy groups

[Tushar Ranjan Moharana]

Thanks a lot Justin.

On Wed, Aug 9, 2017 at 1:33 AM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi All,
> I want to calculate interaction between 2 energy groups, which were not
> defined during the run. So I want to rerun and include both the energy
> groups while rerunning. This can be easily done by again assembling .tpr
> file from .gro, .top and .cpt file by grompp, but I donot have the .gro and
> .cpt file, which I used to compile the original .tpr file. I have topology
> file and run input (.tpr) file and the new trajectory obtained after
> running .tpr file.
>
> Can I convert old .tpr to include energy groups or can I get .cpt and .gro
> used to compile the .tpr file?
>
> I have run many simulation and by mistake the .gro and .cpt file got
> overridden. Kindly suggest if there is any way to achieve the above
> things.
>
> Thanks a lot.
>
>
>
> "A society with free knowledge is better than a society with free food"
> --
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
>



-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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