[gmx-users] Distance restraints

[Justin Lemkul]

On 2/14/13 8:35 AM, Divya Sunil wrote:
> Hello all,
>
> I have been trying to apply distance restraints on my protein. I prepared
> distance restrains using make index and added to topology file. I did it
> just after executing pdb2gmx. Is this the correct procedure to apply
> distance restraints?
>

make_ndx doesn't produce restraints, but if you used an index file as input into 
genrestr -disre, then that's probably correct.  The disre.itp file that will be 
produced will be very generic, with the same restraint distances for everything, 
so that may or may not be correct for whatever it is you're trying to do.  It's 
easy to manually edit, of course.  Bottom line is that a simple test simulation 
and subsequent measurements will tell you if it is working properly.

-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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