Re: [AMBER] bug with amber mask for stability/QH calculations

From: Jason Swails <>
Date: Thu, 20 Nov 2014 18:47:42 -0500

> On Nov 20, 2014, at 6:34 PM, Lawrenz, Morgan <> wrote:
> Hi all,
> I've found a bug in, in the amber mask output when running QH entropy calculations, specifically when a "stability" calculation is performed, i.e. when computing quantities for a single species instead of a complex.
> I found that the Mask() method of the MMPBSA_System class in is printing incorrect amber masks, starting from zero and without the colon (:). I was getting masks in the resulting ptraj scripts like this for a 3 residue peptide:
> matrix mwcovar name comp.matrix ,0-3
> The bug is actually in the method _stability_mask(), the loops and incrementing is off. I put in my own easy fixes but thought I'd bring it to your attention.

Thanks for finding this! Do you happen to have your fix handy so I can add it to the main code?


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 20 2014 - 16:00:03 PST
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