Hey,
I have three small questions/suggestions regarding the
MMPBSA.py/MMPBSA.py.MPI code.
1) search path
==============
I am running a setup consisting of AmberTools 1.5 and Amber 10 -- being
in separate directory trees. MMPBSA.py/MMPBSA.py.MPI did not find
sander, although it's in the $PATH:
> Error: sander could not be found!
I've changed line 587 in MMPBSA.py/MMPBSA.py.MPI to
> sander = utils.which(prog, True)
so that `utils.which` searches in $PATH and not only in $AMBERHOME/bin/.
Is there any problem with this, so it should not be default for all
users? I would consider it a special case if someone really does not
want to use the sander which is in his $PATH (then one still could
temporarily modify the environment).
2) re-implementation of which?
==============================
Isn't it more safe&clean to simply spawn a process with
GNU which instead of trying to re-implement it in the second half of
`utils.which`?
3) MMPBSA.py and MMPBSA.py.MPI
==============================
I did not look at all the implementation details, but it looks it could
be a good idea to somehow get rid of the large part of duplicate code
these two files have. Maintaining two pretty equivalent files probably
requires more effort than necessary :-)
If you're interested, I could work on at least (2).
Thanks for consideration!
Jan-Philip
--
Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 04 2011 - 10:30:03 PDT
