AMBER Archive (2008)

Subject: Re: AMBER: Problems with neglected restaints

From: David A. Case (
Date: Tue Mar 18 2008 - 12:15:56 CDT

On Tue, Mar 18, 2008, wrote:

> *************DISANG FILE (relevant restaints)**********************
> # Asn214 CG to Glu123 CD
> &rst iat= 1945, 3424, nstep1=1,nstep2=100000,
> r1=0.0,r2=0.0,r3=5.7,r4=5.7,
> rk2=50.0, rk3=50.0,
> &end

You cannot set r1=r2, or r3=r4! If you examine the way the restraints are
defined, you will see that this implies there is no restraint. You must
have r4 > r3 (probably by a considerable amount) if you want the upper bound
restraint to be active.

We should probably have sander flag this as an error: I think it checks
if r4 < r3, but not if r4 = r3.

...good luck...dac

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