AMBER Archive (2007)

Subject: Re: Fwd: Re: AMBER: leap restrainTorsion

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 05 2007 - 20:15:36 CST

On Wed, Dec 05, 2007, fatima.chami_at_durham.ac.uk wrote:
>
>
> I started using the NMR approach. My restraint file contains
>
> &rst
> iat= 8, 20, 21, 22,
> r1=160.0,r2=165.8, r3=170.0, r4=171.0,
> rk2=50, rk3=50,
> ialtd=0, &end

You probably need to have r4 much larger, if you want a 180 angle to be
penalized by a significant amount. Try r4 at least at 180.

You should plot your actual penalty function vs. angle to see visually what
regions are allowed and disallowed, and by how much. As others have noticed,
you get counter-intuitive results when r1 is very close to r2, or when r3 is
very close to r4.

>
> I selected iat with respect to sequence number in the Pdb file for the given
> torsion angle
>
> my mdin file:
>
> &cntrl
> imin = 1,
> nmropt = 1,
> pencut=-0.001
> maxcyc = 500,
> ncyc = 250,
> ntb = 0,
> igb = 0,
> cut = 12
> /
> &wt type='REST', istep1=0,istep2=500,value1=0.1,
> value2=1.0, /

As you have seen, it won't work to use variable restraints with minimization:
that only works for MD.

>
> to check if my approach is working i run a minimization
> at current torsional angle of 180.0 which is outside the restraint range

Use the LISTIN=POUT command line to get detailed information on your
restraints.

...hope this helps...dac

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