Hi Ray,
Unless I'm misunderstanding your point, since the second call to MMPBSA.py
with the -use-mdinds flag is what runs the calculation workflow (and from
what I can tell is what removes the mdin2 file), I would still have to add
that copy command somewhere in the mmpbsa python source files.
Joe
------
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/
On Mon, Jun 26, 2017 at 6:48 PM, Ray Luo <rluo.uci.edu> wrote:
> Hi Joe,
>
> How about a quick bypass to save your revised file in a separate
> folder and only copy it over when you want to run the job?
>
> All the best,
> Ray
> --
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 26 2017 - 18:30:03 PDT
