Re: [AMBER] Restraint problem

From: case <>
Date: Wed, 8 Aug 2012 09:30:05 -0400

On Wed, Aug 08, 2012, Fernando Martín García wrote:
> I have a "technical" problem with a distance restraint. I'm working
> with a protein with a 12 angs. TIP3 box. The simulation time is 30 ns.
> After 20 ns, a small part of the protein is out of the box. The problem
> is that one of the residues out of the box has a restrain with one
> residue in the part of the protein inside the water box, so the value
> changes, what it causes a high restraint value. Is there any solution
> for this?

I'm confused by this description. Is the restraint between two atoms in the
same polypeptide chain? If so, the distance should be unaffected by wrapping
or imaging, and have nothing to do with being "outside of the box" or not.
In this case, you need to look more carefully into what might be causing the

(As an aside: protein residues are never really "outside the box"; the may
appear to be that way visually, but periodic images of solvent molecules are
acutally nearby and used in all energy and force calculations.)

If the restraint is between two different "molecules" (e.g. polypeptide
chains), then you need to set iwrap=0 to prevent wrapping from suddenly
changing the distance involved in the restraint. In that case, you may
need to occasionally use cpptraj to center and image the restart file to
make things more compact.

...good luck....dac

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Received on Wed Aug 08 2012 - 07:00:04 PDT
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