On Sep 15, 2012, at 5:10 AM, Dilraj LAMA <dilrajl.bii.a-star.edu.sg> wrote:
> Well so what could be the possible reason? Can someone please help me
> out with both these issues.
>
> 1) The long time for NMODE calculation with MMPBSA.py and
Snapshots must be both minimized and then the hessian needs to be calculated and diagonalized to calculate normal modes. Both steps can take a very long time, so this is not surprising.
> 2) The Index error.
This has already been fixed in the last 2 bug fixes of AmberTools 1.5. Apply all of these bug fixes, reinstall, and use the -rewrite-outputs flag to write the output files.
Also, consider upgrading to AmberTools 12.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Sep 15 2012 - 06:00:03 PDT
