[gmx-users] atom name - topology

[Steven Neumann]

How about exclusions - I want to exclude all non-bonded parameters within
this one residue made of 2500 atoms. Would:

[ moleculetype ]
; Name            nrexcl
  N             2500

Solve the problem? Or shall I create [ exclusions ] part ? Which one would
be faster in terms of performance?

Steven




On Thu, Dec 5, 2013 at 1:41 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> 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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>> Gromacs Users mailing list
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