AMBER Archive (2006)

Subject: Re: AMBER: problem with amber 9 and igb=5

From: David A. Case (
Date: Fri Jun 09 2006 - 16:58:02 CDT

On Thu, Jun 08, 2006, M. Scott Shell wrote:
> Given the fact that our minimization was erratic and not entirely
> reproducible and knowing that many of our initial pdb configurations had
> "perfect" dihedral angles, I decided to perturb all initial pdb phi/psi
> angles by a random amount by up to +- 1 degree. As it turns out, this
> fixed our problem and we no longer saw amber hanging during minimization.

Weird...I can't offhand think of any reason why amber9 would be different
than earlier versions in this respect. The basic routines that work with
angles and torsions haven't changed for many years.

> Might this be due to the minimization procedure itself when symmetries
> are perfect along the backbone, or does this sound like an internal
> coding problem perhaps akin to the acos example mentioned above? We
> haven't seen this problem in amber7 or amber8.

I suppose you could see if MD every hangs with the idealized geometry...that
might help decide if it involves minimization per se, or the way in which
forces are being evaluated.


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