AMBER Archive (2008)

Subject: Re: AMBER: Problems with neglected restaints

From: anna.schrey_at_gmx.de
Date: Thu Mar 20 2008 - 14:43:20 CDT

Thanks!

That was it - r3 < r4 works also with r1 = r2 = 0!

Suggest not to change the latter!

happy holiday @all

Anna
-------- Original-Nachricht --------
> Datum: Tue, 18 Mar 2008 10:15:56 -0700
> Von: "David A. Case" <case_at_scripps.edu>
> An: amber_at_scripps.edu
> Betreff: Re: AMBER: Problems with neglected restaints

> On Tue, Mar 18, 2008, anna.schrey_at_gmx.de 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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