[gmx-users] atom name - topology
s.neumann08 at gmail.com
Thu Dec 5 11:18:22 CET 2013
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
On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul <jalemkul at 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 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
> jalemkul at 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-request at gromacs.org.
More information about the gromacs.org_gmx-users