Re: [AMBER] How to perform backbone and residues restraint at the same time

From: case <>
Date: Fri, 2 Apr 2010 09:57:34 -0400

On Fri, Apr 02, 2010, Rilei Yu wrote:
> Thanks for your help all the time. Now I came across a new problem: I
> want to restraint all the backbone of the protein, while the side
> chain of the residues in the binding site can be flexible. I just want
> to refine the binding modes of my ligand using less time and other
> purpose. Can anyone give me some suggestions?
> I have try many times, but it still does not work well. I find it cannot
> work for my two purposes together.
> ###
> ntr=1, restraintmask=':1-420.CA',
>  /
> Hold the DNA fixed
> 500.0
> RES 1 92
> RES 94-183

You can use either restraintmask OR the group input, not both together.
Note also that 500.00 is way too large a restraint; consider values about 100
times smaller.


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Received on Fri Apr 02 2010 - 07:00:02 PDT
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