Re: [AMBER] Errors in AmberTools14

From: Jonathan Gough <>
Date: Fri, 13 Mar 2015 15:27:23 -0400

I did not download anything from GitHub.

Here is the output of ls from bash

jgough.node4:/scratch1/amber14/AmberTools/src/parmed> ls
chemistry compat24.pyc Makefile parmed.Doxyfile
jgough.node4:/scratch1/amber14/AmberTools/src/parmed> ls * compat24.pyc Makefile parmed.Doxyfile

amber exceptions.pyc __init__.pyc periodic_table.pyc tinker

ParmedTools: argumentlist.pyc changeljpair.pyc gui
        logos.pyc ParmedActions.pyc parmlist.pyc coarsegrain.pyc simulations
addljtype.pyc arraytools.pyc changeradii.pyc
 __init__.pyc mod_molecules.pyc parmed_cmd.pyc exceptions.pyc

I believe that something IS off when the output is parsed by sander. Our
calculations (on the energy) are WAY off. That's how I came across the
errors. The data from one node was correct and the output of the other was

On Fri, Mar 13, 2015 at 3:21 PM, Jason Swails <>

> On Fri, 2015-03-13 at 14:31 -0400, Jonathan Gough wrote:
> > It's ParmEd.... That is where the issue is...
> >
> > I did "clean installs" on 2 nearly identical machines. One worked, one
> > didn't work. how can I trouble shoot that?
> Did you by chance download the Github version of ParmEd on one of those
> machines?
> The thing about ParmEd is that it's Python, so there is no chance of
> there being compiler weirdness causing two machines to yield different
> results from the same code. If one passes tests and the other doesn't,
> then the codes are different.
> I suspect you replaced ParmEd on one of the machines with the version
> from Github, which gives prmtops that differ according to "diff", but
> not according to "sander".
> The ParmEd Github repo has a test/ directory with unit tests that is not
> present in the AmberTools distribution. So if
> $AMBERHOME/AmberTools/src/parmed has a "test" directory, this would
> explain it (and like I mentioned, both versions of ParmEd give
> equivalent topologies, they just look different to dacdif).
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Mar 13 2015 - 12:30:03 PDT
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