[gmx-users] Topology files

[kirtana S]

Thanks for the reply. As I am new to GROMACS I am not able to understand. I
will go through the manual and  will get back if I have further questions.


On Tue, Feb 28, 2012 at 6:00 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> kirtana S wrote:
>
>> Thanks for the documentation. Again I have a  ligand terminated silica
>> nanoparticle ,what can be the easiest way to approach  the topology file
>> for this.
>>
>>
>>
> I don't know what the structure is, but I'll assume the .rtp route is
> probably easier than writing a (presumably) repetitive topology for a
> relatively large particle.  You may or may not need to invoke specbond.dat
> for cross-links, as pdb2gmx can deal only with linear species via .rtp
> entries; other bonds are introduced with specbond.dat.
>
> -Justin
>
>
>> On Tue, Feb 28, 2012 at 5:46 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    kirtana S wrote:
>>
>>        For example if I have a polystyrene polymer chains and monomers
>>        of user defined solvent . I need to construct the .itp file by
>>        hand .
>>
>>
>>    Polystyrene is most easily generated using .rtp entries in pdb2gmx.
>>     The solvent can be described by manually created .itp files.
>>
>>    http://www.gromacs.org/__**Documentation/How-tos/Polymers<http://www.gromacs.org/__Documentation/How-tos/Polymers>
>>    <http://www.gromacs.org/**Documentation/How-tos/Polymers<http://www.gromacs.org/Documentation/How-tos/Polymers>
>> **>
>>
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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