[gmx-users] position restraints

[Justin Lemkul]

On 3/26/13 8:39 AM, Shima Arasteh wrote:
> No, You have not shouted at me, never! But sometimes I think that I deserve to be shouted !!
> I deeply appreciate your patience and attention. Thanks for your time and your replies.
>
> In my protein, chains A and B are identical.
>

If they are identical, then so too should be the position restraint files.  In 
this case, it is still confusing in my mind (really, impossible) that one chain 
gets restrained and the other doesn't.  How are you assessing whether or not the 
restraints are being applied?  Can you quantitatively demonstrate that the 
restraints are not working?  Applying restraints to a protein is a fairly 
rudimentary task, especially when handled by pdb2gmx topologies.

-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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