On Mon, Oct 03, 2016, Maryam Hamzehee wrote:
> I am trying to do MM-PBSA calculation for determining binding energy for
> the complex of receptor and an small ligand. I went through the MMBPSA
> tutorial and used python-based version of MM-PBSA. Unfortunately PB did
> not work, I ignored the PB and continued with GB. After calculation the
> delta G was -4124.0239.
> GENERALIZED BORN:
> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIALTERMS. THE
> VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
Please read the opening paragraphs in Chapter 31 of the Manual. You need to
be able to these calculations "by hand" first. This is (fairly) easy with GB,
since the averages of all the energy terms are printed in the mdout file, and
you just need to subtract the receptor and ligand energies from that of the
complex. This will give you results that you can compare to the results of
the python script, to try to see where the problems are coming from.
(Above ignores contributions from configurational entropy; but you need to
tackle the big problems first.)
...good luck....dac
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Received on Mon Oct 03 2016 - 05:00:03 PDT
