AMBER Archive (2005)

Subject: AMBER: rdparm bug

From: David Mobley (dmobley_at_gmail.com)
Date: Tue Nov 29 2005 - 20:40:02 CST

Hi,

I think there may be a bug in the rdparm module; I'm attaching a
prmtop file which should allow reproduction of the bug.

The exactly problem is that I've set up a small molecule,
benzylacetate, using antechamber and generated prmtop and crd files
with tleap. There are no warnings or anything and the leap log looks
OK. But I run the prmtop file through rdparm (to use with a script
which I won't bother to explain) and the output of rdparm omits LJ
parameters for one of the atom types, "ca". It looks to me like the
parameters are present in the prmtop file but just omitted from the
rdparm file.

Anyway, try running the attached prmtop file through rdparm and seee
for yourself (i.e. printLJ) or see the attached rdparm output file
under the LJ section.

I don't know exactly what triggers the bug; it's certainly not
omitting all "ca" LJ parameters, as I've used this method with other
molecules having "ca" atoms with no problem.

Please let me know if you're able to track it down and come up with a
bugfix. It is fairly important to what I'm doing (I rely on being able
to extract LJ parameters from the rdparm file).

Thanks,
David



-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu