[gmx-users] Topology files

[Justin A. Lemkul]

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>
> 
> 
>     -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>
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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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

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