Re: [AMBER] Distance restraint

From: David A Case <>
Date: Thu, 18 Sep 2014 08:19:55 -0400

On Thu, Sep 18, 2014, John Smith wrote:
> I am trying to construct an adiabatic map for an enzyme ligand complex in
> which the ligand binds covalently to a residue in the protein. I am
> restraining a distance between a ligand atom and a protein atom over a
> range. My input file for minimization looks like this
> #
> # 123 CYM SG 432 UNK C38 1.0 5.3 &rst
> ixpk= 0, nxpk= 0, iat=1937,6833, r1= 0.50, r2= 1.00, r3= 5.30, r4= 5.80,
> rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> &end
> When I run the minimization I only get zero values for the restrain like
> this:

You should expect a zero restraint energy whenever the distance is between
r2 and r3 (i.e. between 1.0 and 5.3). I'm guessing that this is the case for
your initial structure.

You can debug restraints (seeing detailed information about what is being
calculated) by adding a "LISTIN=POUT" card right before or after that "DISANG"

...good luck....dac

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Received on Thu Sep 18 2014 - 05:30:03 PDT
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