[gmx-users] Topology files
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 29 00:00:09 CET 2012
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.
> 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.
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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