[gmx-users] position restraints

Steven Neumann s.neumann08 at gmail.com
Wed Feb 5 14:50:52 CET 2014

In your topology:

; Include Protein topology
#include "protein.itp"

; Include Position restraint file of ligand
#ifdef POSRES
#include "posre_prot.itp"

where posre_prot.itp

; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom  type      fx      fy      fz
1    1    1000    1000    1000

here you specify atoms you wish to restraints from topology of your
molecule in given direction X, Y, Z. The higher the fx, fy, fz the more
stable it will be.
Then in mdp:

define = -DPOSRES


On Wed, Feb 5, 2014 at 1:38 PM, Gurunath Katagi
<gurunath.katagi at gmail.com>wrote:

> Hi everyone,
> I am doing a simulation of a protein using gromacs with charmm forcefields.
> From the crystallographic analysis, it is found that certain residues are
> rigid and few are flexible. I want to apply restraints on these rigid
> residues.
> Can anyone let me know how can I apply restrains on only these rigid
> residues, so that do dont move much during simulation and leave other
> residues without any restraints..
> Thank you
> Gurunath
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