[gmx-users] atom name - topology

[Steven Neumann]

Thank you


On Thu, Dec 5, 2013 at 1:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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