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 <[email protected]
<mailto:[email protected]>> 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>
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<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
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