On Fri, Mar 04, 2016, chemjxn wrote:
> I checked the mmpbsa.out and _MMPBSA_complex_gb.mdout.0 files. No error
> in these two files. In the _MMPBSA_complex_gb.mdout.0, some terms
> equal to '-nan'. The same problem is found in my complexes (about 4
> complexes).
OK, this narrows it down: it looks like there is serious problem with the
complex. You need to solve that problem first. Be sure to read the second
paragraph in the MMPBSA.py Chapter, which I copy here:
"None of these should be considered as a “black-box”, and users should be
familiar with Amber before attempting these sorts of calculations. These
scripts automate a series of calculations, and cannot trap all the types of
errors that might occur. You should be sure that you know how to carry out an
MM-PBSA calculation “by hand” (i.e., without using the scripts); if you don’t
understand in detail what is going on, you will have no good reason to trust
the results. Also, if something goes awry (and this is not all that uncommon),
you will need to run and examine the individual steps to carry out useful
debugging."
[One guess: make sure that there are no bad atom clashes in the complex
coordinates.]
....good luck....dac
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Received on Fri Mar 04 2016 - 06:00:08 PST
