I have not tried as wish to know before loosing time on making the topology. So each atom column needs letters - whats the maximum number of letters? Can I name them with same names (its one residue) as well as in pdb?
Steven On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/4/13 11:48 AM, Steven Neumann wrote: > >> Dear Gmx Users, >> >> My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, >> ACI, GLY and I want to create a topology. Is it possible to make one >> residue of one [ moleculetype ] with this number of atoms so that: >> >> [ moleculetype ] >> ; Name nrexcl >> MOL 3 >> >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass >> typeB chargeB massB >> ; residue 1 1N rtp 1N q 0.0 >> 1 BAS 1 1N 1 1 0 133.208 >> 2 POL 1 1N 2 2 0 87.08 >> 3 NON 1 1N 3 3 0 147.172 >> 4 BAS 1 1N 4 4 0 157.204 >> 5 POL 1 1N 5 5 0 87.08 >> ... >> 2500 POL 1 1N 2500 5 0 87.08 >> >> Can atom column contain number from 1 to 2500? >> >> > Have you tried it? Are you getting some problem? IIRC the atom column > requires a string (name), not an integer. That's what the atom number > column is for. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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.