[gmx-users] atom name - topology

[Justin Lemkul]

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

-- 
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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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