Files sent.
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Jason Swails
Sent: 13 May 2014 12:27
To: amber.ambermd.org
Subject: Re: [AMBER] Alanine Scanning MMPBSA
On Tue, 2014-05-13 at 11:06 +0000, Aronica, Pietro wrote:
> 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?
Can you send me (off-list) the necessary topology files and a shortened
(2-5 frames) trajectory file so I can try to reproduce this behavior?
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 13 2014 - 05:30:02 PDT
