Re: [AMBER] minimization segmentation fault

From: Jorgen Simonsen <>
Date: Fri, 30 Jul 2010 13:11:31 +0200


So I get some very high Gmax value during minimization for a hydrogen
atom(HG2) bound to a Arginine - when I look at the pdb file the distance
between its nearest neighbor is 1.76 to a hydrogen on proline residue

I use constraints for the hydrogen bond length through shake
     ntc = 2, jfastw = 0
     tol = 0.00001

the rms gradient is 5.8 which is pretty high. The vdwaals are negative
-7764. I have not yet added any extra water molecules only the crystal ones
not having too high clashing. Are there any debugging in order to identify
the clash - is it vdw or something else and how to resolve that?

On Tue, Jul 27, 2010 at 8:53 PM, Bill Ross <> wrote:

> > Furthermore, the residues around are displaced which
> > they are not supposed to do - I have included low vdw radii and the
> bonding
> > energy has a very high force constant (100 ) - can I get the clashing
> part
> > of Gmax out?
> The atom indicated by GMAX is the one to focus on.
> What is it? What type? What vdw params? What bonded to?
> Are you expecting that a high bonding force constant will somehow
> compensate for low vdw radii? That would only work in a highly
> constrained system, likely with just a few atoms that could not
> form vdw contacts.
> > When I look in the pdb it seems fine so there is a clash I am
> > not able to see.
> The clash probably develops as atoms are pulled together.
> If you print crds for every step of md or min, you likely will
> see the problem developing.
> Bill
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Fri Jul 30 2010 - 04:30:04 PDT
Custom Search