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Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Mon, Jun 26, 2017 at 2:50 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> 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 - 16:00:02 PDT