[gmx-developers] Re: gmx-developers Digest, Vol 110, Issue 29

[Michel Cuendet]

Hi David, 

As an easy practical workaround until a solution is implemented in gromacs itself, you can use the PLUMED plugin to apply restraints in a molecule-independent way. 

Best, 
Michel


> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sat, 22 Jun 2013 16:36:12 +0000
> From: "Shirts, Michael (mrs5pt)" <mrs5pt at eservices.virginia.edu>
> Subject: [gmx-developers] Re: free energy calculations with restraints
> To: David Mobley <dmobley at gmail.com>, Discussion list for GROMACS
> 	development	<gmx-developers at gromacs.org>
> Message-ID: <CDEB4ABA.20FD9%mrs5pt at eservices.virginia.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> 
> Looking through very briefly, I would think this should be possible to do
> through the pull code.  Basically, you could have an index group with 3 or 4
> atoms, which can then be as angles or dihedrals.
> 
> Anyone with more expertise with the pull code who can comment further as to
> whether this would work?
> 
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
> 
> 
>> From: David Mobley <dmobley at gmail.com>
>> Date: Fri, 21 Jun 2013 13:44:25 -0700
>> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
>> Cc: "Michael R. Shirts" <michael.shirts at virginia.edu>
>> Subject: Re: free energy calculations with restraints
>> 
>> Hi,
>> 
>> Anyone have any insights on this? Do we need to think about implementing
>> angle/torsional restraints in the pull code, or can we re-cast the
>> restraints available within topology files to use absolute atom numbering?
>> 
>> Thanks.
>> 
>> 
>> 
>> On Fri, Jun 14, 2013 at 12:47 PM, David Mobley <dmobley at gmail.com> wrote:
>> 
>>> Hi, devs,
>>> 
>>> I'm writing with an issue relating to the interplay of new free energy
>>> features with restraints.
>>> 
>>> I'm very much appreciating some of the new free energy features in
>>> gromacs, such as the 'couple-moltype' option which provides a way to set up
>>> decoupling or annihilation of a specific molecule via free energy
>>> calculations without having to edit the topology file directly. This is
>>> especially great when it comes to decoupling -- charge decoupling was not
>>> previously possible via topology file editing, and vdW decoupling took
>>> substantial manipulation of the topology file.
>>> 
>>> However, for binding free energies, my work employs orientational
>>> restraints between the protein and ligand. I need to be able to impose both
>>> dihedral and angle restraints on angles between the protein and ligand.
>>> Currently, I do this using angle-restraints and dihedral-restraints. This
>>> requires that both the protein and ligand be within the same logical
>>> 'molecule', which (unfortunately) means that I can't make use of the new
>>> free energy features above, since couple-moltype has to apply to a whole
>>> molecule, not just part of a molecule.
>>> 
>>> So, my I see two possible solutions to the problem, and hence have these
>>> questions:
>>> 1) Can dihedral and angle restraints be applied via the pull code? If not,
>>> are there any plans to add that?
>>> 2) Alternatively, what about modifying the restraints code so it uses (or
>>> at least optionally allows) absolute atom numbering, rather than numbering
>>> within a specific molecule, thus allowing restraints (angle-restraints and
>>> dihedral-restraints) to be applied between 'molecules'?
>>> 
>>> Thanks!
>>> David
>>> 
>>> 
>>> --
>>> David Mobley
>>> dmobley at gmail.com
>>> 949-385-2436
>>> 
>> 
>> 
>> 
>> -- 
>> David Mobley
>> dmobley at gmail.com
>> 949-385-2436
> 
> 
> 
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> 
> End of gmx-developers Digest, Vol 110, Issue 29
> ***********************************************

==========================================================
Michel Cuendet, PhD
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne
Switzerland
http://lausanne.isb-sib.ch/~mcuendet/
==========================================================







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