Thanks Justin. It still doesn't solve my problem, e.g., there are several instances of CT with diferent opls_??? numbers, but no indication of their environments; they could represent C bonded to 1->4 carbon atoms, etc. There's no way of telling. I contacted one of the opls folks last week, but got no response. So I thought I could enlist the help of gromacs users. But thanks for your responses anyway. 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, 7:32 AM > > > Austin B. Yongye wrote: > > 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. > > You don't need it. The corresponding file in 4.0.2 is > called ffoplsaanb.itp. Newer Gromacs versions have a > different directory and naming structure, but the contents > of these files is the same. > > Be aware that there have been dozens (if not hundreds) of > usability upgrades, bug fixes, and new features that have > been added since 4.0.2. You would be well-served to > try to figure out why you can't download a newer version. > > -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, 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 > >> > > -- ======================================== > > 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. 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