Thank you.. I hoped it would be simpler. how do I go about creating unified protein-ligand [moleculartype] directives. Can you suggest any material available on this topic? that would be extremely helpful.
-Saravanan On 28 March 2013 16:45, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/28/13 4:01 AM, Saravanan wrote: > >> Hello everyone, >> >> I am new to using gromacs. I am currently studying an enzyme catalysing a >> transfer reaction. there are two substrates and I want to restraint >> specific interactions between different parts of the ligands and the >> protein. As I understand so far from reading various discussions in the >> group, restraining such interactions is possible through pull code, But we >> can assign only one pull group0, I am wondering if there is better way to >> restraint multiple interactions between multiple molecules in a single >> simulation. If not through pull-code, what will be the best way to ensure >> many specific intermolecular restraints? >> >> > Use distance restraints. Unfortunately, this will require a lot of > topology hacking to create unified protein-ligand [moleculetype] > directives. Restraints (like any bonded interaction) can only be applied > within a [moleculetype], not between them. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists