Thank you
On Thu, Dec 5, 2013 at 1:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/5/13 5:18 AM, Steven Neumann wrote: > >> 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? >> >> > The easiest thing to do is define each residue as if it were a polymer, > then you don't have to worry about 2500+ unique atom names. If each unit > is only a few beads, this becomes trivial to do and pdb2gmx will do all the > work via .rtp entry. > > -Justin > > > 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. >>> >>> > -- > ================================================== > > 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.
