Yeah, those are indeed there for the particular molecules, thanks. I understand that this is the only way to go, it's just that my use of GMX is somewhat different in that I rarely use molecules in the normal sense, and OPLS-AA, being a LEGO for simple groups, has been very convenient with that catalog you mentioned. Like, place a carboxyl termination somewhere, or have a hole in a bulk sheet of graphene, etc.
In any case, thank you. Alex On Wed, Aug 2, 2017 at 12:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/2/17 2:38 PM, Alex wrote: > >> Huh. Most of my work has been with OPLS-AA, so I took that for granted. >> Where would the actual charges be, then? >> >> > In the .rtp file, where residues are defined. Charges are not (and should > not) necessarily be linked to atom types; they are a function of > parametrized groups or molecules. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
