[gmx-users] atom name - topology
jalemkul at vt.edu
Thu Dec 5 14:27:14 CET 2013
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
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.
> 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
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Justin A. Lemkul, Ph.D.
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
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