On Fri, 2014-05-09 at 10:27 +0000, Aronica, Pietro wrote:
> Yes, I can see it. The trajectory itself is fine, but the modified residue has one bond which unrealistically stretches and wobbles way beyond the normal H-C bond length. I assume this is what is causing the error, or is at least a symptom of the true cause. It is the hydrogen that was changed from the rest of the side chain to the hydrogen in alanine. Removing all the atoms in the side chain except for CB and letting leap automatically add the remaining hydrogens does not solve the problem. Looking at the mutated residue in the other three systems shows completely normal behaviour.
> What can cause this, and why is it happening in this system?
Which residue did you try to mutate? And what version of AmberTools are
you using?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 09 2014 - 05:00:02 PDT
