Fwd: Fw: Fwd: [gmx-users] position restraints

[Justin Lemkul]

On 3/16/13 8:34 AM, Shima Arasteh wrote:
> Thanks.
> As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file?
> Do you mean this? Am I right?
>

Yes.  Try it.

> One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command?
>

Type 'help' at the prompt or otherwise search gromacs.org and Google for example 
usage.  It is very easy to create index groups specifying subsets of residues or 
just their backbone atoms, etc.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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