I have upgraded to Amber 14 and AmberTools 14, but that did not solve the issue. I have run more Alanine Scanning on the same peptide, and some residues work fine but some show the same error. Looking at the mdcrd file shows that the mutated amino acid, in case of an error, the system doesn't keep the H-C bond length constant but have it fluctuate randomly, while in the runs that did work the H-C bond is kept at 1.09. As far as I can tell, all files have been generated in exactly the same manner, and the instance of an error is wholly random.
Where can I look to find the source of this issue?
Pietro
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Aronica, Pietro
Sent: 09 May 2014 14:02
To: amber.ambermd.org
Subject: Re: [AMBER] Alanine Scanning MMPBSA
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 Tue May 13 2014 - 04:30:02 PDT
