[gmx-users] atom name - topology

[Justin Lemkul]

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 <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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-- 
==================================================

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

==================================================