The mutation is a leucine to alanine. In the pdb, I deleted everything beyond CG and renamed CG to be HB3. Coincidentally, one the other three mutations I did was also a leucine to alanine mutation, and that one worked fine.
I'm not sure which version of AmberTools I'm running but I'm reasonably certain it should be AmberTools 13.
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Jason Swails
Sent: 09 May 2014 12:43
To: amber.ambermd.org
Subject: Re: [AMBER] Alanine Scanning MMPBSA
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 - 06:30:02 PDT
