Hi Justin,
That makes sense, I've found where the parameters are Thanks for your help James ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 February 2018 22:31:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs On 2/14/18 5:28 PM, Easton J.W. wrote: > Hi Justin, > > Many thanks for the detailed reply. > > I just wanted to check that it doesn't matter that the A2C and A3C are not > present in the bonded and non-bonded itp files for the forcefield? Should > this not have given an error? The topology snippet you showed an [atomtypes] directive with those types defined, so they were in fact in the nonbonded parameter list by virtue of being added just above the first [moleculetype], as is permitted in GROMACS topologies. If there were missing parameters, grompp would have failed with a fatal error, so presumably you also included the necessary bonded parameters somewhere, too. -Justin > Kind regards, > > James > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin > Lemkul <jalem...@vt.edu> > Sent: 14 February 2018 14:43:35 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Potential issue using acpype to convert amber > topology to gromacs > > > > On 2/14/18 9:42 AM, Justin Lemkul wrote: >> >> On 2/14/18 9:33 AM, Easton J.W. wrote: >>> Thanks Justin, >>> >>> >>> Will this effect the interactions (both bonded and non-bonded) that >>> these atoms have, as their atom types are not in the forcefield itp >>> files? >> Missing atom types would cause grompp to fail; you'd never get to the >> point where a simulation would be affected. >> >> You're introducing custom atom types in the topology itself, and >> that's always legal before any [moleculetype] appears. The LJ >> parameters come from the [atomtypes] directive. Masses and charges >> present in that directive aren't used. >> > Actually, to clarify: *if* masses are present in the [atoms] directive > of a [moleculetype], then the masses found in [atomtypes] are not used. > Strictly speaking, it is not necessary to have explicit masses in > [atoms], though nearly all topologies do. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
