On Mon, Nov 14, 2011, Crystal.CHIA-YU Ku wrote:
>
> Besides, acdoctor seemed not to
> run successfully.
[I'm cc-ing this to Junmei: Junmei: please see the attached pdb file, and note
the that acdoctor indeed fails. It seems to think that bondnum is zero, as
well as numh.]
> Now I suspect if the major problem probably is from
> my ligand's pdb file, even if I cannot perceive problems on Chimera
> and AutodockTool.
It is indeed a very strange ligand. It looks like the charge should be -1,
not +1. But it is not just an sqm problem: Gaussian 09 is unable to obtain
SCF convergence on the first step, either. You might try to break the
molecule into smaller pieces to see if that helps: the five-membered ring
is certainly a likely suspect. Others on the list might want to look at the
PDB file to see something.
How did you obtain the pdb file? Did you manipulate it from its original
state?
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 15 2011 - 05:30:03 PST
