AMBER Archive (2005)

Subject: AMBER: Bus error - ambpdb

From: David C. Chan (David.C.Chan_at_dartmouth.edu)
Date: Thu Mar 17 2005 - 08:54:17 CST

Dear Amber users/developers:

I prepared two sets of prmtop and incrd files for an enzyme-cofactor-ligand
complexes (with and without TIP3 waters) to be used in sander and mm_pbsa.
After obtaining the necessary mdcrd files from sander with my solvated system,
I stripped off the waters and counter ions and ran the the mm_pbsa script to
calculate the free energy of the ligand. In the process, ambpdb was invoked and
that was where the calculation halted. I returned to my original prmtop and
incrd for errors. While I obtained a pdb file without any incidence for the
solvated system, the other one (no WAT and counter ions) gave bus error. The
starting pdb (enzyme-cofactor-ligand), frcmod and prep files were all identical
when they went through leap. I repeated with leap again to get the sets of
prmtop and incrd files but it made no difference to the behavior of ambpdb.
Different sets of prmtop and incrd files for combinations like enzyme-cofactor,
enzyme-ligand, enzyme, cofactor and ligand - all worked fine with ambpdb except
the solvent free ternary complexes. Ptraj managed to give me the pdb file in
question but I don't know if this will help my mm_pbsa calculations. Could you
please give me some advise on fixing ambpdb or any workarounds to bypass ambpdb
when running mm_pbsa.pl? Thank you.

Sincerely,

David Chan
Postdoctoral Research Associate
Chemistry Department
6128 Burke Laboratory
Dartmouth College
Hanover NH 03755
Tel: 603 646 9030
Fax: 603 646 3946
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