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-- 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 Tue, Apr 19, 2022 at 10:16 AM Ryan Pavlovicz <pavlovicz.7.osu.edu> wrote: > 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 > > > > > _______________________________________________ > > > > > AMBER mailing list > > > > > AMBER.ambermd.org > > > > > > > > > > > > > > > > > > > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JHUOuRsMd2WTwKo2ys7T_1Xo2e8NmM8TCA-caAWdKakvWkgIyNO0HaET0dggpj7ZVjVA2T3XyBnq1WxBkw3R$ > > > > > > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > > > > > > > > > > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!lFVAK_YKRxnV8Lvr-NgKUrRVrfN0ln1BMZGmrrbFqdSmvNwNeDSCCV0BzwAjK8H05s27$ > > > > > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > > > > > > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JCWkUU4IFYBeF0G40ZBbZOmH4zmkSpG8Y8hhFAAppFQqG509PoRvsXMRGE3Sfu3IxHbgTaZtbvyB5QdpBw$ > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > > > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!gYoweY5VFULXlp3fc18NsU076BTs9pdh5QLfySygC705IVRT0aT17BLmMUPV3G_Aw9WW$ > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!McyB2fqpW4TGoGkASAA4apdyCJXKSm9R4wZFVtKK8nH0S-v61GpT61cY4UOGCsEu7cbausAiyepOuDgPyA$ > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Apr 19 2022 - 17:00:02 PDT