Hi Ray,
I guess that's part of my question/problem. I don't know where the test
cases are or how to run them. The only thing in the manual I see about
tests involve a makefile that isn't part of the conda binary installation
(because no source code).
Is this the issue: "the full source-code distributions are needed if you
wish to combine AmberTools with Amber."
Does mmpbsa need both AmberTools and Amber? You previously mentioned that
sander comes with AmberTools. Are Amber and sander synonymous here?
Thanks again,
ryan
On Mon, Apr 18, 2022 at 4:29 PM Ray Luo <rluo.uci.edu> wrote:
> !-------------------------------------------------------------------|
> This Message Is From an External Sender
> This message came from outside your organization.
> |-------------------------------------------------------------------!
>
> Ryan,
>
> If you can run all the standard mmpbsa.py test cases, you should be fine.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
>
> On Mon, Apr 18, 2022 at 12:40 PM Ryan Pavlovicz <pavlovicz.7.osu.edu>
> wrote:
>
> > Hi Ray,
> >
> > I have had AmberTools21 installed via the directions here:
> >
> >
> https://urldefense.com/v3/__http://ambermd.org/GetAmber.php*ambertools__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!JCWkUU4IFYBeF0G40ZBbZOmH4zmkSpG8Y8hhFAAppFQqG509PoRvsXMRGE3Sfu3IxHbgTaZtbvw6ijGWiA$
> >
> > conda create --name AmberTools21
> > conda activate AmberTools21
> > conda install -c conda-forge ambertools=21 compilers
> > conda update -c conda-forge ambertools
> >
> > I have been successfully been using this installation to use cpptraj, but
> > would now like to use MMPBSA.py as well.
> >
> > I don't see how I can test this binary installation, particularly the
> > mmpbsa.py test as you suggest. Could you point me in the right direction?
> >
> > Thanks for your help,
> >
> > ryan
> >
> > On Sat, Apr 16, 2022 at 8:00 AM Ray Luo <rluo.uci.edu> wrote:
> >
> > > !-------------------------------------------------------------------|
> > > This Message Is From an External Sender
> > > This message came from outside your organization.
> > > |-------------------------------------------------------------------!
> > >
> > > Ryan,
> > >
> > > Here is my suggestion, download and install AmberTools 2021 and make
> sure
> > > all tests, especially the mmpbsa.py tests pass. Note sander is part of
> > > AmberTools, so mmpbsa should be able to run even if you don't have an
> > Amber
> > > license.
> > >
> > > All the best,
> > > Ray
> > > --
> > > Ray Luo, Ph.D.
> > > Professor of Structural Biology/Biochemistry/Biophysics,
> > > Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> > > Biomedical Engineering, and Materials Science and Engineering
> > > Department of Molecular Biology and Biochemistry
> > > University of California, Irvine, CA 92697-3900
> > >
> > >
> > > On Thu, Apr 14, 2022 at 6:26 PM Ryan Pavlovicz <pavlovicz.7.osu.edu>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I am trying to run an MMPBSA calculation on a trajectory that was
> > > generated
> > > > via OpenMM with an Amber force field:
> > > >
> > > > cpptraj found! Using /opt/conda/envs/AmberTools21/bin/cpptraj
> > > >
> > > > mmpbsa_py_energy found! Using
> > > > /opt/conda/envs/AmberTools21/bin/mmpbsa_py_energy
> > > >
> > > > Preparing trajectories for simulation...
> > > >
> > > > File "/opt/conda/envs/AmberTools21/bin/MMPBSA.py", line 4, in
> > <module>
> > > >
> > > > __import__('pkg_resources').run_script('MMPBSA.py==16.0',
> > > 'MMPBSA.py')
> > > >
> > > > File
> > > >
> > > >
> > >
> >
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/pkg_resources/__init__.py",
> > > > line 662, in run_script
> > > >
> > > > self.require(requires)[0].run_script(script_name, ns)
> > > >
> > > > File
> > > >
> > > >
> > >
> >
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/pkg_resources/__init__.py",
> > > > line 1466, in run_script
> > > >
> > > > exec(script_code, namespace, namespace)
> > > >
> > > > File
> > > >
> > > >
> > >
> >
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/EGG-INFO/scripts/MMPBSA.py",
> > > > line 99, in <module>
> > > >
> > > > File
> > > >
> > > >
> > >
> >
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/MMPBSA_mods/main.py",
> > > > line 167, in file_setup
> > > >
> > > > self.mut_str, mutant_residue = make_mutant_trajectories(INPUT,
> > FILES,
> > > >
> > > > File
> > > >
> > > >
> > >
> >
> "/opt/conda/envs/AmberTools21/lib/python3.9/site-packages/MMPBSA.py-16.0-py3.9.egg/MMPBSA_mods/make_trajs.py",
> > > > line 298, in make_mutant_trajectories
> > > >
> > > > from alamdcrd import MutantMdcrd, GlyMutantMdcrd
> > > >
> > > > ModuleNotFoundError: No module named 'alamdcrd'
> > > >
> > > > I have AmberTools installed via conda but do not have an Amber/sander
> > > > install (no license). Should I be able to successfully run MMPBSA.py
> > with
> > > > only an AmberTools installation?
> > > >
> > > > Thanks,
> > > >
> > > > ryan
> > > > _______________________________________________
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> > > >
> > >
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Received on Tue Apr 19 2022 - 10:30:02 PDT
