Justin: I am using gromacs version 4.0.2. Several attempts to download current gromacs versions from http://www.gromacs.org/Downloads kept yielding 93.0-byte files. So I re-installed my pre-existing v4.0.2 without any problems (>./configure --enable-sse; make; make install). If you could send me the ffnonbonded.itp file that would be great. Austin-
--- On Tue, 4/5/11, Justin A. Lemkul <jalem...@vt.edu> wrote: > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] OPLS-AA atom types > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Tuesday, April 5, 2011, 6:06 AM > > > Austin B. Yongye wrote: > > Thanks Justin. > > Could you/someone please forward the file? I don't > have it. > > It's part of your Gromacs installation. > $GMXLIB/oplsaa.ff/ffnonbonded.itp. > > If you don't have it, then Gromacs wasn't properly > installed and you won't be > able to use whatever force field for which you're designing > your topologies. > > -Justin > > > Austin- > > > > --- On Tue, 4/5/11, Justin A. Lemkul <jalem...@vt.edu> > wrote: > > > >> From: Justin A. Lemkul <jalem...@vt.edu> > >> Subject: Re: [gmx-users] OPLS-AA atom types > >> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > >> Date: Tuesday, April 5, 2011, 5:19 AM > >> > >> > >> Austin B. Yongye wrote: > >>> Hello GROMACS USERS, > >>> Does any one have a document/manual/link that > >> describes the name-number atom type mappings > employed in > >> opls-aa? > >> The correspondence between the atom types and > bonded types > >> is all contained in ffnonbonded.itp. > >> > >> -Justin > >> > >>> I would like to build some molecules and > specify their > >> parameters, but I see different of numbers for the > same atom > >> type name, e.g: > >>> TYPE NAME > >>> 135 CT > >>> 136 CT > >>> 137 CT > >>> 157 CT > >>> > >>> I can deduce that 135 is CH3-, 136 is R-CH2-, > and 137 > >> is RRCH- by looking at topology files. > >>> Thanks, > >>> Austin- > >> -- ======================================== > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> MILES-IGERT Trainee > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> 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 > >> 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 > >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > 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 > 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 > -- 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
