[AMBER] MMPBSA.py bug with amber mask for stability/QH calculations

From: Lawrenz, Morgan <mlawrenz.amgen.com>
Date: Thu, 20 Nov 2014 23:34:06 +0000

Hi all,
I've found a bug in MMPBSA.py, 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 parm_setup.py 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.
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Received on Thu Nov 20 2014 - 16:00:02 PST
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