Re: [AMBER] Restrained MD

From: David A Case <>
Date: Sun, 29 Mar 2015 10:42:50 -0400

On Sun, Mar 29, 2015, James Starlight wrote:
> I would like to perform such kind of the restrained MD during which I
> need to constrain dihedral angle of side-chain of selected residue
> within very narrow range (e.g between 80-120 degrees). Should I use
> here options used for the umbrella simulations or there is another
> more trivial methods (e.g using some sort of NMR constraints etc)?

It sounds like you want "NMR" restraints (which are often used for purposes
other than NMR refinement.) You can have a "flat well" between 80 and 120 (so
any value in there will have the same energy), and penalties to keep the
system from moving outside that range.


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Received on Sun Mar 29 2015 - 08:00:02 PDT
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