Hi all,
We've been trying to do a protein/DNA mmpbsa calculation using the
non-linear PB (so running with use_sander = 1, -make-mdins, then -use-mdins
to mmpbsa.py). We are using AmberTools17.
We are trying to do the calculation on 50 frames over several trajectories.
After getting to about frame 8 in the analysis (for both of our
trajectories), the output from the calculation starts giving
PBSA WARNING in pb_miccg(): CG maxitn exceeded!
We increase the verbosity and we increased the maxitn to a very large
number (1,000,000) in one of the calcs, and still get the same problem. The
warning appears to come after the output
Atomic solvent accessible surface area:
in the output files consistently. Looking at the mdcrd trajectory that
mmpbsa produces for the calculation, there is no obvious difference in
between say frame 7 and 8 in the trajectory that would suggest why the
calculation is getting stuck all of sudden.
Linear PB and GB handle the same sets of frames just fine by the way.
I can provide more detailed information (input scripts, info about the
system, etc.) if needed.
Thanks,
Joe
------
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
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Received on Sat Jul 01 2017 - 19:30:02 PDT
