[AMBER-Developers] leap error

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 2 Jun 2011 12:45:13 -0400

Hello everyone,

So in the course of a discussion with someone from the Amber list, it
appears as though the error in which ATOMS_PER_MOLECULE doesn't add up to
NATOM (giving rise to uninitialized molecule ownership lists and segfaults
for pressure scaling/imaging) *is* actually caused by leap.

I've attached a zipped archive of the files that were sent to me. The
following python script will show you what I'm talking about:


from chemistry.amber.readparm import amberParm

l = amberParm('NDM.prmtop')

print 'NATOM = %d' % (l.ptr('natom'))

print 'sum ( ATOMS_PER_MOLECULE ) = %d' %


Execute this script like:

$AMBERHOME/bin/python test_script.py.

I'm guessing something funky is happening because of the bond commands that
link the Zinc atoms. These should probably be built into the libraries
themselves, but this still shouldn't be making leap create a seg-faulting

Unfortunately, gmail doesn't like the .lib suffix, so the OP sent me files
renamed from .lib to _lib.txt, and .frcmod to _frcmod.txt, so renaming these
files to the original suffix is necessary to get the leap_batch script to
run correctly. Then,

tleap -f leap_batch

produces the offending prmtop.

This has actually raised another issue that I will post about shortly.

Any questions, please ask.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate

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Received on Thu Jun 02 2011 - 10:00:04 PDT
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