Hi all,
We have been doing some calculations with MMPBSA.py which require us to
invoke the use_sander = 1 option and to make some modifications to the
_MMPBSA_pb.mdin files (we have been following some suggestions on a
previous Amber mailing list thread for protein/DNA calculations).
We went through and gave the -make-mdins flag the first time to MMPBSA.py,
and then the -use-mdins flag the second time, and found that the
calculation kept failing when it tried to find a file called
_MMPBSA_pb.mdin2 in the directory to use (error messages to our output are
pasted below). This file was in the directory after using the -make-mdins
flag, but we noticed that it disappeared as soon as the -use-mdins flag was
called in the second run of MMPBSA.py with our modified mdin files.
I seem to have been able to "fix" this by tracking down in the
amber16/lib/python2.7/site-packages/MMPBSA_mods a file called utils.py
which has a section in it that is called to decide which files to keep when
the -use-mdins flag is passed to MMPBSA.py (line 45 of that python script
in the AmberTools17 version of the script). It did not include mdin2 in the
list of files. So long story short, we just tried editing the utils.py file
to also keep the mdin2 file, reran our calculations and then everything
worked fine (meaning everything ran without giving errors).
My question is whether this is okay or not to have done? I assume that if
mdin2 file was not being kept in the utils.py script, there was probably a
reason for it?
Thanks for your input.
Joe
---error messaging from output log before modifying the utils.py script---
Loading and checking parameter files for compatibility...
sander found! Using /share/apps/amber16/bin/sander
cpptraj found! Using /share/apps/amber16/bin/cpptraj
Preparing trajectories for simulation...
2 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /share/apps/amber16/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
File "/share/apps/amber16/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File
"/share/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/share/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 81, in run
calc.setup()
File
"/share/apps/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 199, in setup
raise IOError("Input file (%s) doesn't exist" % self.input_file)
IOError: Input file (_MMPBSA_pb.mdin2) doesn't exist
Exiting. All files have been retained.
------
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
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Received on Mon Jun 26 2017 - 15:00:02 PDT
