[gmx-users] virtual sites

Roland Schulz roland at utk.edu
Tue Oct 29 21:38:04 CET 2013

On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:

> Dear Users,
> I have a system consisting of peptides and a linear carbohydrate.
> Initially I tried to simulate these peptides using virtual sites and
> it worked. I can use pdb2gmx for building virtual sites on protein
> whereas I have an itp file for the carbohydrate.

Yes you can modify the top file by hand to use itp files generated in two
different ways.

> Is it possible to
> apply virtual site to a carbohydrate along with the peptides?
If you have an rtp file for you carbohydrate you should be able to run
pdb2gmx and then you should also be able to generate vsite. Or you can
generate them using your own scripts. Of course you only need them if you
have the respective groups (e.g. CH3).


> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
> --
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