AMBER Archive (2005)

Subject: AMBER: ambpdb core dump

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Fri Jul 29 2005 - 06:27:46 CDT

All:
 
I'm having a problem with ambpdb. I made a residue (so this is not a
standard base or amino acid). In xleap, I made top/crd and pdb files.
This was done without complaint from xleap. The top and crd files were
used for a MM run which completed successfully and a rst file was
written. I attempted to make a pdb file with the original top and rst
files....
 
ambpdb -p XXX.top < XXX.rst > XXX.pdb
 
and get a core dump. I did manage to get the result open in moil-view
but when moil-view writes a pdb, it changes all the atom types to DUMM.
No matter, the stucture looks OK.
 
I went back and tried to make a pdb from the original top/crd files.
Same result, a core dump.
 
I tried some other top/crd combinations from files for both standard
residues and homemade ones without difficulty so the executable does not
seem to be the problem. My home made residue contains a porphyrin and a
zinc, in case that has anything to do with it.
 
Anyone have an idea of what the problem might be? I'm quite perplexed
that ambpdb can't put back together a top/crd file that xleap
generated.
 
Thanks.
Pete
 
 

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