I have run the same calculation with a different but similar system (it has a staple between two residues) and I see the same error as before: when it generates the trajectory for the mutated complex, the newly created alanine has unrealistic dynamics. Furthermore, this happens in the same residue (146) while not happening in the ones that didn't have an error even in systems without the staple (143-145 and 147). I have not checked the other residues that give this error, but I expect them to show the same behaviour.
I have then run the same calculation on an older version of AmberTools. I'm not sure which one it is, but the command
MMPBSA --version
returns 2.7. This calculation runs fine, generating a completely reasonable trajectory for the mutated complex and giving no error whatsoever.
Clearly, the error is within the new version of the protocol, which, in some consistent cases, fails to give proper results.
I hope this can be fixed somehow.
Cheers
Pietro
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Aronica, Pietro [pietro.aronica07.imperial.ac.uk]
Sent: 13 May 2014 13:01
To: 'AMBER Mailing List'
Subject: Re: [AMBER] Alanine Scanning MMPBSA
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 20 2014 - 06:30:05 PDT
