Okay, clearer now. Will see what I can do. Thanks a lot for your help. Massimo
2013/8/19 Justin Lemkul <jalem...@vt.edu> > > > On 8/19/13 10:22 AM, massimo sandal wrote: > >> 2013/8/19 Justin Lemkul <jalem...@vt.edu> >> >> >>> >>> >>>> An .itp is just a topology, so it's identical to a .top except that it >>> does not have system-level directives and does not #include a parent >>> force >>> field. Manual sections 5.7.1 and 5.7.2 describe the relevant contents. >>> >>> >>> >>> I know - just to be sure we're understanding each other, I know it's >> identical to a *GROMACS* .top , not the CNS one. :) >> >> In 5.7.1 and 5.7.2 yes,there is description of the topology file format, >> but I'm unsure what you precisely meant with the ffbonded.itp / charge >> groups stuff you said I have to refer in. >> > > Run something through pdb2gmx with Gromos96 and you will see what I mean. > For instance, in [bonds] each atom pair must have a gb_* term that > corresponds to the bonded parameters. Unlike OPLS, AMBER, etc. the bonded > parameters are not simply looked up when using Gromos96. Therefore, you > have to match your atom types to their numbers, then look up the > appropriate gb_*, ga_*, gd_*, and gi_* entries from ffbonded.itp. In the > CNS .top files I was looking at, there are no charge groups. You will need > to find a way to assign them. Gromos96 uses charge groups to break down > chemical functional groups. > > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > 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
