Hi,
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.
Best
Junmei
Received on Sun Jul 27 2008 - 06:07:13 PDT
