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

[Shima Arasteh]

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?

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?


Thanks in advance.

Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, March 16, 2013 3:39 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/16/13 7:09 AM, Shima Arasteh wrote:
> Do you mean that I need to make 2 backbone_posre.itp files for 2 chains?
> It would not be possible because I don't see any option for seperate chains when running genrestr command.
>

You need to provide a sensible index group to genrestr to create such groups.

-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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