Re: [AMBER] Restrained MD

From: David A Case <>
Date: Mon, 30 Mar 2015 11:19:30 -0400

On Mon, Mar 30, 2015, James Starlight wrote:
> 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 ?

Be sure to read Section 23.1 of the Reference Manual. You can set nmropt=1
and add something like the following to the DISANG file:

 &wt iat=?,?,?,?, r1=70., r2=80., r3=100., r4=110., rk2=??., rk3=??, /

Here the iat's are the atom numbers that identify the torsion you wish to
constraint, and the values of rk2 and rk3 depend on how steep a penalty you
wish to have when the torsion is outside the allowed value of 80 - 100 deg.
You will probably have to run some test simulations to get a idea of what
these should be.


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Received on Mon Mar 30 2015 - 08:30:12 PDT
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