As a follow-up, I've been using the older version of MMPBSA (2.7) as a replacement for now. It gives results that are comparable to those of the newer version. The magnitude and the error of the deltas for both native and mutant are very similar, as well as the magnitude of the delta delta. However, the error of the delta delta is huge, ten times what it is in the newer version.
To make an example, this is the MMPBSA calculation on the same trajectory.
Newer version:
Native: -53.8694 +/- 7.2906
Mutant: -49.1516 +/- 7.2006
Delta delta: -4.7178 +/- 1.0669
Older version:
Native: -53.8586 +/- 7.2821
Mutant: -49.1035 +/- 7.1908
Delta delta: -4.7551 +/- 10.2341
Why is the error so large? Is it calculated in a different way?
Kind regards
Pietro
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Jason Swails [jason.swails.gmail.com]
Sent: 20 May 2014 14:33
To: amber.ambermd.org
Subject: Re: [AMBER] Alanine Scanning MMPBSA
On Tue, 2014-05-20 at 13:21 +0000, Aronica, Pietro wrote:
> 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.
I've run your example and I have reproduced the problem. The alanine
scanning code has not changed appreciably since it was written ~5 years
ago. I still haven't been able to track down the root cause, but when
it is fixed it is likely that only AmberTools 14 will receive the
update.
Thanks,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 28 2014 - 07:00:02 PDT
