Re: [gmx-users] Combining various Flat-bottomed Potentials

[Jagannath Mondal]

Hi
  I am also interested in the issue of using a  flat-bottomed restraint,
for a spherocylinder.
 However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.

If we put the spherical and cylindrical restraint on the same particle
(under the [position restraints] flag as Justin and Chris has suggested ),
the particle will be either be in a spherical confinement or in a
cylindrical confinement .  But for a spherocylinder, we need two
hemispheres which are capped on the two ends of a cylinder.
Hence, for a spherocylindrical restraint, what is needed here is a
restraint which will restrain the particle on going out when the z
coordinate of the particle exceeds the diameter of the cylinder AND the
sqrt(x**2+y**2) of the particle exceeds the length of the cylinder.
I am wondering whether this is possible within the current gromacs
implentation.
If it is not, I was interested in editing the source code relevant for flat
bottomed potential, to implement it for a spherocylinder. Is the following
path within gromacs directory right place to make the changes ?
  gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c

Any suggestions will be welcome.
Thanks

On Wed, May 25, 2016 at 2:22 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Thanks for the clarification Justin.
>
> Those interested in using these potentials (as I was) should be careful as
> I think that at lease some forms are broken when using domain decomposition:
> http://redmine.gromacs.org/issues/1969
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: 24 May 2016 12:33:54
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Combining various Flat-bottomed Potentials
>
> On 5/24/16 12:30 PM, Christopher Neale wrote:
> > I doubt it. The flat-bottom potential in the pull-code is not really the
> standard definition of a flat-bottom potential. In my opinion, a
> flat-bottom potential has a low, and a high defined value and then the
> restraint increases harmonically above high and below low with no penalty
> between low and high set values. However, the gromacs 5.1.2 flat-bottom
> potential is simply a regular potential where the forces are set to zero
> below the central set point and there is a harmonic above the central set
> point. I'd call this a half-harmonic rather than a flat-bottom potential.
> Luckily, the code is quite simple to modify to get a proper flat-bottom
> potential, which you could use to get your cylinder.
> >
> > You want to modify src/gromacs/pulling/pull.cpp around line 1129 and
> remove the code:
> >
> >  if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
> > {
> > dev = 0;
> > }
> >
> > And replace it with:
> >
> >if (pcrd->params.eType == epullFLATBOTTOM)
> > {
> > if (dev > -1 && dev <1){
> >   dev = 0;
> > } else {
> >   if (dev >0){
> > dev-=1;
> >   }else {
> > dev+=1;
> >   }
> > }
> > }
> >
> > That will give you a flat-bottom width of 2.0 nm (1 nm on each side).
> This is the quick and dirty approach where you just hard-code your
> potential flat-bottom width then compile it like that. You will need to
> change the "1" in four places if you want a different width.
> >
>
> If I understand the OP correctly, this isn't a matter of using the pull
> code,
> rather simultaneously using flat-bottom options in [position_restraints].
> It
> should be possible to simply combine the available options to whatever the
> user
> desires.  Several people have asked the same question in recent days, yet
> it
> doesn't seem like anyone's actually *tried* to do it yet.  That would be a
> much
> more useful effort :)
>
> -Justin
>
> > Obviously test it also prior to production.
> >
> > Chris.
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Srajan
> Jain 
> > Sent: 24 May 2016 05:13:17
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Combining various Flat-bottomed Potentials
> >
> > Dear Gromacs users,
> >
> > I want to impose a sphero-cylinderical position restraint, using
> > flat-bottomed potentials, for a simulation.
> >
> > The manual mentions that we can combine the existing three flat-bottomed
> > potentials, like a cylinder with two layers to get a disk.
> >
> > So, can this feature be used to generate a sphero-cylinder?
> >
> > Thank you in advance.
> > --
> > Gromacs Users mailing list
> >
> > * Please 

Re: [gmx-users] Combining various Flat-bottomed Potentials

[jagannath mondal]

Hi
  I am also interested in the issue of using a  flat-bottomed restraint,
for a spherocylinder.
 However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.

If we put the spherical and cylindrical restraint on the same particle
(under the [position restraints] flag as Justin and Chris has suggested ),
the particle will be either be in a spherical confinement or in a
cylindrical confinement .  But for a spherocylinder, we need two
hemispheres which are capped on the two ends of a cylinder.
Hence, for a spherocylindrical restraint, what is needed here is a
restraint which will restrain the particle on going out when the z
coordinate of the particle exceeds the diameter of the cylinder AND the
sqrt(x**2+y**2) of the particle exceeds the length of the cylinder.
I am wondering whether this is possible within the current gromacs
implentation.
If it is not, I was interested in editing the source code relevant for flat
bottomed potential, to implement it for a spherocylinder. Is the following
path within gromacs directory right place to make the changes ?
  gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c

Any suggestions will be welcome.
Thanks
Jagannath

On Wed, May 25, 2016 at 2:22 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Thanks for the clarification Justin.
>
> Those interested in using these potentials (as I was) should be careful as
> I think that at lease some forms are broken when using domain decomposition:
> http://redmine.gromacs.org/issues/1969
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: 24 May 2016 12:33:54
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Combining various Flat-bottomed Potentials
>
> On 5/24/16 12:30 PM, Christopher Neale wrote:
> > I doubt it. The flat-bottom potential in the pull-code is not really the
> standard definition of a flat-bottom potential. In my opinion, a
> flat-bottom potential has a low, and a high defined value and then the
> restraint increases harmonically above high and below low with no penalty
> between low and high set values. However, the gromacs 5.1.2 flat-bottom
> potential is simply a regular potential where the forces are set to zero
> below the central set point and there is a harmonic above the central set
> point. I'd call this a half-harmonic rather than a flat-bottom potential.
> Luckily, the code is quite simple to modify to get a proper flat-bottom
> potential, which you could use to get your cylinder.
> >
> > You want to modify src/gromacs/pulling/pull.cpp around line 1129 and
> remove the code:
> >
> >  if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
> > {
> > dev = 0;
> > }
> >
> > And replace it with:
> >
> >if (pcrd->params.eType == epullFLATBOTTOM)
> > {
> > if (dev > -1 && dev <1){
> >   dev = 0;
> > } else {
> >   if (dev >0){
> > dev-=1;
> >   }else {
> > dev+=1;
> >   }
> > }
> > }
> >
> > That will give you a flat-bottom width of 2.0 nm (1 nm on each side).
> This is the quick and dirty approach where you just hard-code your
> potential flat-bottom width then compile it like that. You will need to
> change the "1" in four places if you want a different width.
> >
>
> If I understand the OP correctly, this isn't a matter of using the pull
> code,
> rather simultaneously using flat-bottom options in [position_restraints].
> It
> should be possible to simply combine the available options to whatever the
> user
> desires.  Several people have asked the same question in recent days, yet
> it
> doesn't seem like anyone's actually *tried* to do it yet.  That would be a
> much
> more useful effort :)
>
> -Justin
>
> > Obviously test it also prior to production.
> >
> > Chris.
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Srajan
> Jain 
> > Sent: 24 May 2016 05:13:17
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Combining various Flat-bottomed Potentials
> >
> > Dear Gromacs users,
> >
> > I want to impose a sphero-cylinderical position restraint, using
> > flat-bottomed potentials, for a simulation.
> >
> > The manual mentions that we can combine the existing three flat-bottomed
> > potentials, like a cylinder with two layers to get a disk.
> >
> > So, can this feature be used to generate a sphero-cylinder?
> >
> > Thank you in advance.
> > --
> > Gromacs Users mailing list
> >
> 

[gmx-users] Simulating conjugated protein

[Sanket Ghawali]

Dear, gmx-users,

Hello everyone,

I'm simulating a peptide in an SDS micelle, where my peptide is conjugated
to a organic compound at the N terminal. The SDS micelle was genrated using
CHARMM-GUI, here I am stuck with a problem for adding atom types for the
compound. I tried adding atomtypes for the compound into the .rtp files of
the CHARMM forcefield but when i try to run pdb2gmx it throws an error
regarding missing residues in .hdb file.

I edited the .hdb file adding the hydrogen atom information for the unknown
compound. The pdb2gmx worked this time but it throws back an error while
adding ions.

I tried using SwissParam to parameterized the unknown molecule, using this
i find that the compound does not remain bound to the peptide at the N
terminal even after merging the compound and peptide co ordinates.

The errors which i get while adding ions:

ERROR 190 [file topol.top, line 3284]:
  No default Proper Dih. types


ERROR 191 [file topol.top, line 3285]:
  No default Proper Dih. types


ERROR 192 [file topol.top, line 3286]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'SDS'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 1 [file topol.top, line 3377]:
  System has non-zero total charge: 17.180007
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.




---
Program grompp, VERSION 4.6.5
Source code file: /root/Downloads/gromacs-4.6.5/src/kernel/grompp.c, line: 563

Fatal error:
number of coordinates in coordinate file (sol.gro, 15465)
 does not match topology (topol.top, 15450)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Being Great is Not So Good" (Red Hot Chili Peppers)

.


Any suggestions on how to go about doing this?


Thanks,

Sanket
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Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Tsjerk Wassenaar]

Hi Sourav,

For Martini there's the conversion script martinize, which has an option
-nt to suppress putting charges on termini.

This is not really a Gromacs question, and it's better to post Martini
related questions on the forum at http://cgmartini.nl

Cheers,

Tsjerk
On May 24, 2016 23:35, "Justin Lemkul"  wrote:

>
>
> On 5/24/16 5:33 PM, Sourav Ray wrote:
>
>> Hello
>>
>> Thanks for your answer, I presume pdb2gmx needs some force-field
>> definitions to work, anyway, can I assign charges selectively to certain
>> atom  number? Let me know if it is feasible, I searched the forums but
>> couldn't find anything specific.
>>
>>
> Try some MARTINI tutorials; IIRC topology generation is not typically done
> via pdb2gmx.
>
> -Justin
>
> Regards
>> Sourav
>>
>> On Wed, May 25, 2016 at 2:48 AM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> If you've already arranged your own termini, then you can choose "None"
>>> from the options pdb2gmx presents.
>>>
>>> Mark
>>>
>>> On Tue, May 24, 2016 at 11:15 PM Sourav Ray 
>>> wrote:
>>>
>>> Hello

 I am trying to put selective charges on the termini, I am getting stuck

>>> at
>>>
 the initial stage where I am supposed to mention the force-field needed.

>>> As
>>>
 martini termini differ from conventional ones, I am unable to bypass
 NH3+
 or COO- termini options at the start and end respectively as there is no
 appropriate force-field option present there. Please let me know if

>>> anyone
>>>
 has a workaround.

 Regards
 Sourav
 --
 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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 --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
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>>> posting!
>>>
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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
>
> ==
> --
> 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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Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Justin Lemkul]

On 5/24/16 5:33 PM, Sourav Ray wrote:

Hello

Thanks for your answer, I presume pdb2gmx needs some force-field
definitions to work, anyway, can I assign charges selectively to certain
atom  number? Let me know if it is feasible, I searched the forums but
couldn't find anything specific.



Try some MARTINI tutorials; IIRC topology generation is not typically done via 
pdb2gmx.


-Justin


Regards
Sourav

On Wed, May 25, 2016 at 2:48 AM, Mark Abraham 
wrote:


Hi,

If you've already arranged your own termini, then you can choose "None"
from the options pdb2gmx presents.

Mark

On Tue, May 24, 2016 at 11:15 PM Sourav Ray  wrote:


Hello

I am trying to put selective charges on the termini, I am getting stuck

at

the initial stage where I am supposed to mention the force-field needed.

As

martini termini differ from conventional ones, I am unable to bypass NH3+
or COO- termini options at the start and end respectively as there is no
appropriate force-field option present there. Please let me know if

anyone

has a workaround.

Regards
Sourav
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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] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Sourav Ray]

Hello

Thanks for your answer, I presume pdb2gmx needs some force-field
definitions to work, anyway, can I assign charges selectively to certain
atom  number? Let me know if it is feasible, I searched the forums but
couldn't find anything specific.

Regards
Sourav

On Wed, May 25, 2016 at 2:48 AM, Mark Abraham 
wrote:

> Hi,
>
> If you've already arranged your own termini, then you can choose "None"
> from the options pdb2gmx presents.
>
> Mark
>
> On Tue, May 24, 2016 at 11:15 PM Sourav Ray  wrote:
>
> > Hello
> >
> > I am trying to put selective charges on the termini, I am getting stuck
> at
> > the initial stage where I am supposed to mention the force-field needed.
> As
> > martini termini differ from conventional ones, I am unable to bypass NH3+
> > or COO- termini options at the start and end respectively as there is no
> > appropriate force-field option present there. Please let me know if
> anyone
> > has a workaround.
> >
> > Regards
> > Sourav
> > --
> > 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.
> >
> --
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> posting!
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>
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[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Sourav Ray]

Hello

I am trying to put selective charges on the termini, I am getting stuck at
the initial stage where I am supposed to mention the force-field needed. As
martini termini differ from conventional ones, I am unable to bypass NH3+
or COO- termini options at the start and end respectively as there is no
appropriate force-field option present there. Please let me know if anyone
has a workaround.

Regards
Sourav
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Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Mark Abraham]

Hi,

If you've already arranged your own termini, then you can choose "None"
from the options pdb2gmx presents.

Mark

On Tue, May 24, 2016 at 11:15 PM Sourav Ray  wrote:

> Hello
>
> I am trying to put selective charges on the termini, I am getting stuck at
> the initial stage where I am supposed to mention the force-field needed. As
> martini termini differ from conventional ones, I am unable to bypass NH3+
> or COO- termini options at the start and end respectively as there is no
> appropriate force-field option present there. Please let me know if anyone
> has a workaround.
>
> Regards
> Sourav
> --
> 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.
>
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[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Sourav Ray]

Hello

I am trying to put selective charges on the termini, I am getting stuck at
the initial stage where I am supposed to mention the force-field needed. As
martini termini differ from conventional ones, I am unable to bypass NH3+
or COO- termini options at the start and end respectively as there is no
appropriate force-field option present there. Please let me know if anyone
has a workaround.

Regards
Sourav
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Re: [gmx-users] Combining various Flat-bottomed Potentials

[Christopher Neale]

Thanks for the clarification Justin.

Those interested in using these potentials (as I was) should be careful as I 
think that at lease some forms are broken when using domain decomposition:
http://redmine.gromacs.org/issues/1969


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: 24 May 2016 12:33:54
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Combining various Flat-bottomed Potentials

On 5/24/16 12:30 PM, Christopher Neale wrote:
> I doubt it. The flat-bottom potential in the pull-code is not really the 
> standard definition of a flat-bottom potential. In my opinion, a flat-bottom 
> potential has a low, and a high defined value and then the restraint 
> increases harmonically above high and below low with no penalty between low 
> and high set values. However, the gromacs 5.1.2 flat-bottom potential is 
> simply a regular potential where the forces are set to zero below the central 
> set point and there is a harmonic above the central set point. I'd call this 
> a half-harmonic rather than a flat-bottom potential. Luckily, the code is 
> quite simple to modify to get a proper flat-bottom potential, which you could 
> use to get your cylinder.
>
> You want to modify src/gromacs/pulling/pull.cpp around line 1129 and remove 
> the code:
>
>  if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
> {
> dev = 0;
> }
>
> And replace it with:
>
>if (pcrd->params.eType == epullFLATBOTTOM)
> {
> if (dev > -1 && dev <1){
>   dev = 0;
> } else {
>   if (dev >0){
> dev-=1;
>   }else {
> dev+=1;
>   }
> }
> }
>
> That will give you a flat-bottom width of 2.0 nm (1 nm on each side). This is 
> the quick and dirty approach where you just hard-code your potential 
> flat-bottom width then compile it like that. You will need to change the "1" 
> in four places if you want a different width.
>

If I understand the OP correctly, this isn't a matter of using the pull code,
rather simultaneously using flat-bottom options in [position_restraints].  It
should be possible to simply combine the available options to whatever the user
desires.  Several people have asked the same question in recent days, yet it
doesn't seem like anyone's actually *tried* to do it yet.  That would be a much
more useful effort :)

-Justin

> Obviously test it also prior to production.
>
> Chris.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Srajan Jain 
> 
> Sent: 24 May 2016 05:13:17
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Combining various Flat-bottomed Potentials
>
> Dear Gromacs users,
>
> I want to impose a sphero-cylinderical position restraint, using
> flat-bottomed potentials, for a simulation.
>
> The manual mentions that we can combine the existing three flat-bottomed
> potentials, like a cylinder with two layers to get a disk.
>
> So, can this feature be used to generate a sphero-cylinder?
>
> Thank you in advance.
> --
> 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.
>

--
==

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] Release of FESetup 1.2

[Hannes Loeffler]

Hello everyone,

we are delighted to announce the release of FESetup 1.2.

FESetup is a tool to automate the setup of (relative) alchemical free
energy simulations like thermodynamic integration (TI) and free energy
perturbation (FEP) as well as post–processing methods like MM–PBSA and
LIE.  FESetup can also be used for general simulation setup
("equilibration") through an abstract MD engine.  The latest releases
are available from our project web page at
http://www.hecbiosim.ac.uk/fesetup

Release notes can be found at
https://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/wiki/?pagename=Releases


Many thanks,
Hannes Loeffler.
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Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

[Teemu Murtola]

Hi,

On Tue, May 24, 2016 at 8:22 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Thank you for the help. After a but of fiddling your suggestion did lead
> to the solution:
>
> echo -e "\"group_&_1\"\n\"group_&_2\" | gmx ...
>
> Is this really what you had in mind?


That will work, although you will have less escaping if you use single
quotes like

echo -e '"group_&_1"\n"group_&_2"' | gmx ...

or

gmx rdf -ref '"group_&_1"' -sel '"group_&_2"' ...


> If so, I think I'll still submit a feature request since I doubt we can
> expect all users to come up with that on their own.


This is documented in the help that you can access with 'help syntax' in
the interactive selection prompt, or, e.g., here: <
http://manual.gromacs.org/documentation/5.1.2/onlinehelp/selections.html#selection-syntax
>

"Strings that contain non-alphanumeric characters should be enclosed in
double quotes as in the examples."

It is impractical to write a parser that can guess what the user tries to
mean with all kinds of weird strings that can have other meanings; what
would you, for example, expect to happen if you create an index group named
"x-y<3" or "resname GLY", and then just type that as the selection, without
quotes? Treating some punctuation characters differently from others would
not provide a very intuitive syntax, either...

I think a reasonable resolution for such a feature request would be to add
an explicit example of selecting such a group in the selection examples.

And if you think make_ndx creates groups that are inconveniently named and
you cannot robustly rename them, you can use gmx select to create exactly
the same groups (with the exception of the splitting options in make_ndx),
and also provide names for them in one go.


> Also, interactive selection is not available with all tools (see e.g. gmx
> traj).
>

I'm not sure what you are referring to with this. Yes, the selection syntax
is not available for all tools, and that is a valid reason to use index
files. But for tools that support them, I think it is still clearer to pass
the selections as command-line arguments instead of piping them. And there
are cases where it is very difficult to pipe the proper selections.

Best regards,
Teemu
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Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

[Christopher Neale]

Dear Teemu:

Thank you for the help. After a but of fiddling your suggestion did lead to the 
solution:

echo -e "\"group_&_1\"\n\"group_&_2\" | gmx ...

Is this really what you had in mind? If so, I think I'll still submit a feature 
request since I doubt we can expect all users to come up with that on their 
own. Also, interactive selection is not available with all tools (see e.g. gmx 
traj).

Thank you,
Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Teemu Murtola 

Sent: 20 May 2016 23:33:36
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Invalid selection near '&' syntax error -- easy way to 
avoid?

Hi,

On Sat, May 21, 2016 at 1:09 AM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> I find that gmx make_ndx will create groups with names that have
> ampersands in them and that this complicates piping the group name back
> into an analysis tool. I have included an example below. There is an
> obvious solution with sed to rename the group in the .ndx file after
> creation (this is what I am doing now). However, I'm thinking about posting
> a redmine feature request since ideally I think the tool will not require
> an external step for name-based selection and I wanted to ask here first
> just in case I am missing something.
>

Three points:

   - If you need to select a group with non-alphanumeric names in gmx rdf
   or other selection-enabled tools, you simply need to put the group name in
   double quotes.
   - There is no need to pipe the selections to gmx rdf. You can simply
   write "gmx rdf -ref '' -sel ''", which at least to me is
   much more obvious.
   - There can be cases where writing an intermediate index file is
   justified, but for one-off groups, it is easier to just specify them
   directly to gmx rdf or other tools as a static selection like "name A B and
   resname 1 to 64", passed directly to the command-line options. Or if you
   need to reuse the same selection multiple times, you can put it in a file
   and pass it using -sf (like -ref -sf myselection.txt, or even -ref -sel -sf
   myselection.txt, which reads both selections from the same file).

Best regards,
Teemu
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Re: [gmx-users] small molecule aggregation analysis

[Justin Lemkul]

On 5/24/16 12:19 PM, Surahit Chewle wrote:

Hello Everyone,

I have simulated a system of 10 synthetic drug molecules (each 20 atoms) in
small organic solvent, methanol on Gromacs 4.6.5

as far as I have read, there are many tools available for protein
aggregation, but if you can suggest a tool of choice for small molecule
aggregation, for ex, radial distribution function that will be helpful.

Fairly new to Gromacs and this is my first post, so kindly be gentle if I
have made a mistake posting this message.



I don't think there's necessarily any tool that is predisposed to being intended 
for protein aggregation; most of the analyses applied in those cases are rather 
generic - contacts, distance matrices, buried SASA, possibly RDF, 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] Combining various Flat-bottomed Potentials

[Justin Lemkul]

On 5/24/16 12:30 PM, Christopher Neale wrote:

I doubt it. The flat-bottom potential in the pull-code is not really the 
standard definition of a flat-bottom potential. In my opinion, a flat-bottom 
potential has a low, and a high defined value and then the restraint increases 
harmonically above high and below low with no penalty between low and high set 
values. However, the gromacs 5.1.2 flat-bottom potential is simply a regular 
potential where the forces are set to zero below the central set point and 
there is a harmonic above the central set point. I'd call this a half-harmonic 
rather than a flat-bottom potential. Luckily, the code is quite simple to 
modify to get a proper flat-bottom potential, which you could use to get your 
cylinder.

You want to modify src/gromacs/pulling/pull.cpp around line 1129 and remove the 
code:

 if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
{
dev = 0;
}

And replace it with:

   if (pcrd->params.eType == epullFLATBOTTOM)
{
if (dev > -1 && dev <1){
  dev = 0;
} else {
  if (dev >0){
dev-=1;
  }else {
dev+=1;
  }
}
}

That will give you a flat-bottom width of 2.0 nm (1 nm on each side). This is the quick 
and dirty approach where you just hard-code your potential flat-bottom width then compile 
it like that. You will need to change the "1" in four places if you want a 
different width.



If I understand the OP correctly, this isn't a matter of using the pull code, 
rather simultaneously using flat-bottom options in [position_restraints].  It 
should be possible to simply combine the available options to whatever the user 
desires.  Several people have asked the same question in recent days, yet it 
doesn't seem like anyone's actually *tried* to do it yet.  That would be a much 
more useful effort :)


-Justin


Obviously test it also prior to production.

Chris.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Srajan Jain 

Sent: 24 May 2016 05:13:17
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Combining various Flat-bottomed Potentials

Dear Gromacs users,

I want to impose a sphero-cylinderical position restraint, using
flat-bottomed potentials, for a simulation.

The manual mentions that we can combine the existing three flat-bottomed
potentials, like a cylinder with two layers to get a disk.

So, can this feature be used to generate a sphero-cylinder?

Thank you in advance.
--
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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] Combining various Flat-bottomed Potentials

[Christopher Neale]

I doubt it. The flat-bottom potential in the pull-code is not really the 
standard definition of a flat-bottom potential. In my opinion, a flat-bottom 
potential has a low, and a high defined value and then the restraint increases 
harmonically above high and below low with no penalty between low and high set 
values. However, the gromacs 5.1.2 flat-bottom potential is simply a regular 
potential where the forces are set to zero below the central set point and 
there is a harmonic above the central set point. I'd call this a half-harmonic 
rather than a flat-bottom potential. Luckily, the code is quite simple to 
modify to get a proper flat-bottom potential, which you could use to get your 
cylinder.

You want to modify src/gromacs/pulling/pull.cpp around line 1129 and remove the 
code:

 if (pcrd->params.eType == epullFLATBOTTOM && dev < 0)
{
dev = 0;
}

And replace it with:

   if (pcrd->params.eType == epullFLATBOTTOM)
{
if (dev > -1 && dev <1){
  dev = 0;
} else {
  if (dev >0){
dev-=1;
  }else {
dev+=1;
  }
}
}

That will give you a flat-bottom width of 2.0 nm (1 nm on each side). This is 
the quick and dirty approach where you just hard-code your potential 
flat-bottom width then compile it like that. You will need to change the "1" in 
four places if you want a different width.

Obviously test it also prior to production.

Chris.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Srajan Jain 

Sent: 24 May 2016 05:13:17
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Combining various Flat-bottomed Potentials

Dear Gromacs users,

I want to impose a sphero-cylinderical position restraint, using
flat-bottomed potentials, for a simulation.

The manual mentions that we can combine the existing three flat-bottomed
potentials, like a cylinder with two layers to get a disk.

So, can this feature be used to generate a sphero-cylinder?

Thank you in advance.
--
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[gmx-users] small molecule aggregation analysis

[Surahit Chewle]

Hello Everyone,

I have simulated a system of 10 synthetic drug molecules (each 20 atoms) in
small organic solvent, methanol on Gromacs 4.6.5

as far as I have read, there are many tools available for protein
aggregation, but if you can suggest a tool of choice for small molecule
aggregation, for ex, radial distribution function that will be helpful.

Fairly new to Gromacs and this is my first post, so kindly be gentle if I
have made a mistake posting this message.


many thanks,
Surahit
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Re: [gmx-users] angle_restraint_z

[Justin Lemkul]

On 5/24/16 10:36 AM, Karina wrote:

Hello,

I am trying to restrain the angle between two atoms (type a5) in a half
spherical body with respect to the z axis. I am trying to use
angle_restraint_z, but not sure how to do it correctly due to lack of
information in the manual or in forums.

I have created a .itp file with  angle_restraint_z and included it in the
topology file as follows:

#include "a5.itp"
#ifdef ANGRESZ
#include "angrez-a5.itp"
#endif

and in the .mdp file as follows:
define   =-DANGRESZ

The problem is I get the following error

Fatal error:
[ file angrez-a5.itp, line 5 ]:
Atom index (3384) in angle_restraints_z out of bounds (1-1).
This probably means that you have inserted topology section "angle_restraints_z"
in a part belonging to a different molecule than you intended to.
In that case move the "angle_restraints_z" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

The only way I can run it is if my indexes are 1 in my .itp file:

[ angle_restraints_z ]
;i j   funct   theta0   fc   mult
 1 119010  1

which is incorrect.

Can you please help me understand how to do it correctly?



Angle restraints are like any other restraints and are numbered based on 
[moleculetype] number, not global atom number:


http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

Likely you've inserted your #include statement after your #include 
(whatever).ff/ions.itp" or something similar that has only 1-atom [moleculetypes].


-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] ?==?utf-8?q? SAS for membrane protein

[Maximilien LOPES RODRIGUES]

> The calculation group is protein + membrane, then choose just the protein for
> output.
> 
> -Justin


Hi Justin, thanks for replying so fast.

So I have to create a group protein + membrane using index.ndx but I don't 
understand how to output the protein only.
With the command gmx sasa, I just can choose the group of calculation and after 
that the program is already terminated, giving me a .xvg file and .pdb file.
Can you explain me more steps please ?

Thank you again !
Kind regards,
Max

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Re: [gmx-users] SAS for membrane protein

[Justin Lemkul]

On 5/24/16 8:43 AM, Maximilien LOPES RODRIGUES wrote:

Hi dear gromacs users,

It's the first time I use this mail list, I hope it will work fine.

I have simulated a membrane protein in a lipid bilayer with water etc. 
Everything is fine but I now want to calculate the accessible surface of the 
protein. Can you help me to understand how does it work ?

I obviously have a .gro (or .pdb) containing the system and an index file to 
select only the protein, lipids,...
"gmx sasa" is the command to use. But I don't know how to only calculate the 
SAS of the part of the protein that is effectively in contact with water ? I mean, we 
have to exclude the hydrophobic surface that is in contact with lipids.



The calculation group is protein + membrane, then choose just the protein for 
output.


-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] SAS for membrane protein

[Maximilien LOPES RODRIGUES]

Hi dear gromacs users,

It's the first time I use this mail list, I hope it will work fine.

I have simulated a membrane protein in a lipid bilayer with water etc. 
Everything is fine but I now want to calculate the accessible surface of the 
protein. Can you help me to understand how does it work ?

I obviously have a .gro (or .pdb) containing the system and an index file to 
select only the protein, lipids,...
"gmx sasa" is the command to use. But I don't know how to only calculate the 
SAS of the part of the protein that is effectively in contact with water ? I 
mean, we have to exclude the hydrophobic surface that is in contact with lipids.

Is my question understandable ?

Thank you in advance. Hope I can help in return.
Kind regards,
Max
-- 
Maximilien LOPES RODRIGUES
PhD student 

Département de Chimie
Chimie-Physique des Biomolécules (CPB)

Tel. +32 (0)81 72 45 23
Fax. +32 (0)81 72 45 46

maximilien.lopesrodrig...@unamur.be
https://directory.unamur.be/staff/mlopesro

Université de Namur
Rue de Bruxelles 61 - 5000 Namur
Belgique 

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Re: [gmx-users] Deprotonated Asp and Glu

[sun]

Allright Thank you very much for quick response. 

Sent from my iPhone

> On 24-May-2016, at 6:05 pm, "Smith, Micholas D."  wrote:
> 
> Best thing to do would be to check the *.gro and *.top files and see if it 
> really is deprotonated.
> 
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of sun 
> 
> Sent: Tuesday, May 24, 2016 8:33 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Deprotonated Asp and Glu
> 
> The charge on Asp amd Glu seems 0 and hydrogens are present in time frames 
> and cluster.pdb. But I deprotonated during pd2gmx.
> 
> Sent from my iPhone
> 
>> On 24-May-2016, at 6:00 pm, sun  wrote:
>> 
>> Hello
>> I have simulated a protein ligand complex and analyzed the trajectory. After 
>> visualization of time frames and clusters.pdb; It occurs to me that the Asp 
>> and Glu are nit deprotonated although during pdb2gmx I used -inter command 
>> and deprotonated both residue according to pH 7. Can anyone tell me if this 
>> possible during visualization? or what might the problem be? My protein is 
>> Amyloid beta peptide (1-42) and ligand is a small organic molecule (35 
>> atoms), Gromacs 5.0 and ff Gromos96 43A1.
>> With Regards
>> Suniba
>> 
>> Sent from my iPhone
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Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

[Justin Lemkul]

On 5/23/16 5:31 AM, zeineb SI CHAIB wrote:

I'm looking to generate the topology of a HEM protein , I choose CHARMM as a 
force field. At the begining, when I run pdb2gmx I had this error about missing 
hydrogen's:

WARNING:
atom HA is missing in residue HEM 473 in the pdb file

You
might need to add atom HA to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)






WARNING:
atom HB is missing in residue HEM 473 in the pdb file

You
might need to add atom HB to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)









---
Program
pdb2gmx, VERSION 4.6.5
Source
code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line:
1588



Fatal
error:
There
were 30 missing atoms in molecule Other2, if you want to use this
incomplete topology anyhow, use the option -missing
For
more information and tips for troubleshooting, please check the
GROMACS
website
at http://www.gromacs.org/Documentation/Errors
---
After a research, I found what was missing: I made a copy of aminoacids.hdb 
(Charmm27.ff folder) in my working directory and I edited this file:
I added the following Lines:



The .hdb file must still be in the force field directory (wherever that may be, 
$GMXLIB or working directory), not in the working directory itself.  Otherwise 
it will have no effect.













HEME 16

1
  1   HA
 CHA C1A C4D
1
  1   HB
 CHB C4A C1B
1
  1   HC
 CHC C1C C4B
1
  1   HD
 CHD C1D C4C
3
  4   HMA
CMA C3A C2A
2
  6   HAA
CAA C2A
CBA
2
  6   HBA
CBA CAA
CGA
3
  4   HMB
CMB C2B C1B
1
  1   HAB
CAB C3B CBB
2
  3   HBB
CBB CAB C3B
3
  4   HMC
CMC C2C C1C
1
  1   HAC
CAC CBC C3C
2
  3   HBC
CBC CAC C3C
3
  4   HMD
CMD C2D C1D
2
  6   HAD
CAD C2D CBD
2
  6   HBD
CBD CAD CGD



I fixed the problem of missing hydrogens but I'm having another type of error:

Special Atom Distance matrix:
  HEM360  HEM360
CAB2CAC3
  HEM360CAC3   0.796
  HEM360FE43   0.557   0.557

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file: 
/home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, 
line: 645

Fatal error:
Residue 'HEM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I added an entry in residuetype.dat (HEM  Protein), after making a copy in 
my working directory but it didn't fix the problem. I verified each file and 
they seem OK, I can't find where is the problem!!! Any help please!!!



The residue name is HEME, not HEM (specbond.dat changes it).

-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] Deprotonated Asp and Glu

[Smith, Micholas D.]

Best thing to do would be to check the *.gro and *.top files and see if it 
really is deprotonated.

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of sun 

Sent: Tuesday, May 24, 2016 8:33 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Deprotonated Asp and Glu

The charge on Asp amd Glu seems 0 and hydrogens are present in time frames and 
cluster.pdb. But I deprotonated during pd2gmx.

Sent from my iPhone

> On 24-May-2016, at 6:00 pm, sun  wrote:
>
> Hello
> I have simulated a protein ligand complex and analyzed the trajectory. After 
> visualization of time frames and clusters.pdb; It occurs to me that the Asp 
> and Glu are nit deprotonated although during pdb2gmx I used -inter command 
> and deprotonated both residue according to pH 7. Can anyone tell me if this 
> possible during visualization? or what might the problem be? My protein is 
> Amyloid beta peptide (1-42) and ligand is a small organic molecule (35 
> atoms), Gromacs 5.0 and ff Gromos96 43A1.
> With Regards
> Suniba
>
> Sent from my iPhone
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Re: [gmx-users] ffbonded.itp

[Justin Lemkul]

On 5/24/16 6:20 AM, a.om...@shirazu.ac.ir wrote:

​Hi
I want to simulate a glycoprotein, I have defined a new residue with charmm36
I should define some angles, bonds and dihedrals for this new residue in 
ffbonded.itp file,
also in the ffbonded.itp file there is some other numbers and etc
I dont know what are these and how to define correctly these parametres for my 
sugar in my protein


Start with Chapter 5 of the manual.

-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] Deprotonated Asp and Glu

[Justin Lemkul]

On 5/24/16 8:30 AM, sun wrote:

Hello I have simulated a protein ligand complex and analyzed the trajectory.
After visualization of time frames and clusters.pdb; It occurs to me that the
Asp and Glu are nit deprotonated although during pdb2gmx I used -inter
command and deprotonated both residue according to pH 7. Can anyone tell me
if this possible during visualization? or what might the problem be? My


The simulation won't do anything you don't tell it.  Asp and Glu are 
deprotonated by default in pdb2gmx, so there should be no need to do anything to 
them.  Probably you made the wrong choice when setting up the topology.  The 
contents of the topology are definitive; if you're seeing unexpected "bonds" in 
a visualization software, those are typically guessed from the coordinates and 
are not necessarily real (e.g. nearby water/ligand H might get "bonded" to an 
Asp/Glu).


-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] help required in calculation of domain decomposition for a mixed lipid vesicle system

[Justin Lemkul]

On 5/24/16 6:35 AM, Antara mazumdar wrote:

Dear gromacs users,


I am trying to calculate domain decomposition of a mixed lipid vesicle
system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to
run in parallel.

I want to calculate the number of PME nodes per total number of nodes.
However, i am not clear on how to calculate the value of nPME here. I would
also mention that number of nodes that can be used need to be multiple of
16 and the value of minimum cell size is 1.8 nm.

Can someone guide me in this regard?


Is there something wrong with the number of PME nodes that mdrun sets up by 
default?

-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] Deprotonated Asp and Glu

[sun]

The charge on Asp amd Glu seems 0 and hydrogens are present in time frames and 
cluster.pdb. But I deprotonated during pd2gmx.

Sent from my iPhone

> On 24-May-2016, at 6:00 pm, sun  wrote:
> 
> Hello 
> I have simulated a protein ligand complex and analyzed the trajectory. After 
> visualization of time frames and clusters.pdb; It occurs to me that the Asp 
> and Glu are nit deprotonated although during pdb2gmx I used -inter command 
> and deprotonated both residue according to pH 7. Can anyone tell me if this 
> possible during visualization? or what might the problem be? My protein is 
> Amyloid beta peptide (1-42) and ligand is a small organic molecule (35 
> atoms), Gromacs 5.0 and ff Gromos96 43A1.
> With Regards
> Suniba
> 
> Sent from my iPhone
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[gmx-users] Deprotonated Asp and Glu

[sun]

Hello 
I have simulated a protein ligand complex and analyzed the trajectory. After 
visualization of time frames and clusters.pdb; It occurs to me that the Asp and 
Glu are nit deprotonated although during pdb2gmx I used -inter command and 
deprotonated both residue according to pH 7. Can anyone tell me if this 
possible during visualization? or what might the problem be? My protein is 
Amyloid beta peptide (1-42) and ligand is a small organic molecule (35 atoms), 
Gromacs 5.0 and ff Gromos96 43A1.
With Regards
Suniba

Sent from my iPhone
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[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

[Antara mazumdar]

Dear gromacs users,


I am trying to calculate domain decomposition of a mixed lipid vesicle
system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to
run in parallel.

I want to calculate the number of PME nodes per total number of nodes.
However, i am not clear on how to calculate the value of nPME here. I would
also mention that number of nodes that can be used need to be multiple of
16 and the value of minimum cell size is 1.8 nm.

Can someone guide me in this regard?
Kind Regards,
Antara

--
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Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
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[gmx-users] ffbonded.itp

[a . omidi]

​Hi
I want to simulate a glycoprotein, I have defined a new residue with charmm36
I should define some angles, bonds and dihedrals for this new residue in 
ffbonded.itp file,
also in the ffbonded.itp file there is some other numbers and etc
I dont know what are these and how to define correctly these parametres for my 
sugar in my protein
could you help me
Thanks

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