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.
Cheers, Tsjerk On Wed, Apr 15, 2009 at 9:05 AM, Hitesh singla <[email protected]> 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 > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
