On Wed, Jul 23, 2008, Junmei Wang wrote:
>
> When I ran mm_pbsa.pl (amber10 and amber11) for a protein complex (using
> delphi), I always found a warning message saying the net charge of the
> ligand is not an integer. At the beginning I though it was something wrong
> with the charge file, but I ended up finding the pdb files generated by
> mm_pbsa.pl are not good: one atom name is missing and another atom name
> showing up twice. Because the output of delphi are automatically deleted, it
> is rather difficult to catch this bug.
Problems reports for mm_pbsa are becoming increasingly common, and Holger (or
his group) have not been responding to these, or providing updates. I don't
use this program myself, so I can't be of much help.
Junmei: please file a bug report on bugzilla, so this doesn't get lost.
Is there anyone else with mm_pbsa experience who can take over some aspects of
responding to problems in this area?
...thanks!...dave
Received on Sun Jul 27 2008 - 06:07:15 PDT
