Dear AMBERers,
I am trying to use the MMPBSA.py script to do MM-PBSA calculation for my systems. The amber package I have is amber 10.
Although the test runs are all passed, I notice that all the *.mdout file are not completed. They all stuck at the following part:
"--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1"
I found that imin=5 is used in the GB/PB calculation. But then I also found the following in the amber10 manual:
"imin=5 In &cntrl. Trajectory analysis is not supported."
Can I use imin=1 instead of imin=5 here? If yes, how can I change it in the MMPBSA.py script? I really appreciate your help.
Thanks,
Wei
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Received on Mon Jan 03 2011 - 09:00:03 PST
