On Mon, Jul 1, 2013 at 9:11 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> You shouldn't be trying to execute the scripts in the source directory. Do
> MMPBSA.py and MMPBSA.py.MPI exist in your $AMBERHOME/bin/ directory? If
> those files do not exist in your $AMBERHOME/bin/ directory, it sounds like
> they weren't ever installed properly. Also, have you tried the calculation
> in serial to make sure it will work? You should always try it in serial
> before attempting the calculations in parallel.
>
> The errors you are seeing are not caused by the AmberTools version you are
> using, per se, but there are upgrades and fixes to MMPBSA.py in general
> that would be available only with upgrading to AmberTools 12. Also, you
> would not need to re-run your MD simulations after upgrading to AmberTools
> 12, just the MMPBSA.py calculations.
>
Minor correction for clarity here -- the latest version is AmberTools 13
(and that is available for free download at
http://ambermd.org).
The installation procedure for AmberTools 13 is drastically simpler than
that for AmberTools 1.5.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 01 2013 - 08:30:03 PDT
