[gmx-users] How to restrain ligand atom position

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 15 09:11:40 CEST 2009

Hi Hitesh,

The posre.itp file only contains a header [ position_restraints ]
followed by a list of atom numbers and restraint force constants.
Check chapter 5 of the manual for how and what. For a ligand it's
probably best to directly add the [ position_restraints  ] section in
the file with the [ molecule_type ] definition, possibly enclosed by
the statements #ifdef POSRES and #endif. Mind that the aom numbers
need to refer to the atom numbers within the molecule_type definition
and are not related to the atom numbers in the coordinate file.



On Wed, Apr 15, 2009 at 9:05 AM, Hitesh singla
<hiteshsingla123 at gmail.com> wrote:
> Dear all,
> I have generated .itp file for ligand using PRODRG server which i included
> in topology file. Now for position restrained dynamics, i wanted to restrain
> atom positions for ligand and protein . But porse.itp which generated using
> pdb2gmx contain restraints for protein only. Kindly provide me the solution
> to restrain ligand atoms.
> Thanks,
> Hitesh Singla
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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