Hello,
On Sun, Oct 3, 2010 at 2:17 AM, Anuradha Mittal
<anuradha.mittal.gmail.com>wrote:
> Hi,
>
> I am trying to run MM-PBSA calculations using mmpbsa.py script but I am
> getting the following errors.
>
> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified
> Bondi radii (mbondi)
> forrtl: Input/output error
> forrtl: severe (38): error during write, unit 16, file
>
/cfs/scratch/users/amitta2/fabh/lig6/restrt
>
This is a problem that pops up every once in awhile when running
MMPBSA.py.MPI. It's due to the fact that different threads are running
concurrent sander instances but don't specify a restart file, so "restrt" is
written by all. This occasionally leads to this error if two threads are
doing just the right (wrong?) things at just the right times. I've fixed
this error by specifying a unique restart to each thread, but I haven't
created/posted the bugfix yet. The current workaround is to use the
non-parallel version. I'll work on getting a patch out this week to fix
this issue, and check back with you when it's available.
Thanks!
Jason
> Traceback (most recent call last):
> File "/u/ac/amitta2/amber11/bin/MMPBSA.py.MPI", line 1571, in <module>
> decompout, idecomp, dec_verbose, ligstart, decomprun, surften,
> cavity_surften, temp)
> File "/u/ac/amitta2/amber11/src/mmpbsa_py/utils.py", line 4595, in
> PrintFinalResults
> '',finaloutput, debug, numframes, one_trajectory,verbose) # noalascan is
> [avg,stdev]
> for total DELTA G
> File "/u/ac/amitta2/amber11/src/mmpbsa_py/utils.py", line 1694, in
> gboutput
> bonddif[x] = bonddif[x] - bond[x]
> IndexError: list index out of range
>
> Looking forward for some suggestions to fix the problem
>
> Thanks
> Anu
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Oct 03 2010 - 15:00:04 PDT
