Re: [AMBER] Errors in AmberTools14

From: Jason Swails <>
Date: Fri, 13 Mar 2015 15:21:24 -0400

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

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).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 13 2015 - 12:30:03 PDT
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