[gmx-users] atom name - topology

[Steven Neumann]

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 <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
>
> --
> ==================================================
>
> 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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