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 <jalem...@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

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Justin A. Lemkul, Ph.D.
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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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