Re: [AMBER] Restrained MD

From: James Starlight <>
Date: Mon, 30 Mar 2015 14:38:46 +0200

Yes, in theory it seems correct!

could someone provide with some example of such realization
considering my task (e.g just to restrain CHI-1 side-chain dihedral
angle of specified residue within it range of +80 to +100 degrees)?
I've found only such example in Refinement of a DNA Duplex tutorial
which seems for me allitle tricky :-) Is it possible just to define
all nessesary inputs within file using mnropt flag for
instance ?


2015-03-29 16:42 GMT+02:00 David A Case <>:
> 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.
> ....dac
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Received on Mon Mar 30 2015 - 06:00:39 PDT
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