AMBER Archive (2005)

Subject: Re: AMBER: ambpdb core dump

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 29 2005 - 09:40:03 CDT

On Fri, Jul 29, 2005, Peter Gannett wrote:
>
> 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.

Have you applied bugfix.29? If so, you should post the top and rst files,
and we will see if we can reproduce this.

> but when moil-view writes a pdb, it changes all the atom types to DUMM.

(This is a little confusing, since pdb files don't contain atom-type
information.)

...dac
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