AMBER Archive (2009)

Subject: Re: [AMBER] QQD psuedoatom restraints

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Jun 15 2009 - 07:00:23 CDT

On Fri, Jun 12, 2009, Titus, Jamie (bairdje) wrote:
>
> Per our previous discussion on QQD psuedoatom restraints, I would also
> like to make sure an unusual arginine restraint would work properly as
> well.
>
> If I modify the map.DG-AMBER file with the following line:
>
> QQHH = CZ 2.1
>
> which was calculated by computing the distance between the CZ atom of
> arginine to each of the atoms 1HH1, 1HH2, 2HH1, and 2HH2, taking the
> longest distance of the four, and adding a twentieth of an angstrom.
>
> Will this restraint work properly during sander, and is this the proper
> way to include a restraint to this degenerate chemical shift?

I think you have to decide for yourself what is "proper". Generate some
configurations that have contacts to the arginine that you would like to
allow, and some that you think would not qualify. Then see whether the
restraint generated with the QQHH pseudoatom does a reasonable job of
disriminating between allowed and disallowed conformations.

...good luck...dac

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