On Sun, Oct 17, 2004, Cai, Yufeng wrote:
>
> I am trying to use antechamber to generate a prep file for my chemical
> compound from PDB structure and here is what I met:
>
> "Cannot successfully assign bond type for this molecule, please double
> check the structure (the connectivity) and/or adjust atom valence
> penalty parameters in APS.DAT"
>
> And in the output (prepi) file, it only includes part of the compound's
> atoms.
Also, double-check that every atom has a unique name in the input pdb file.
This is especially true for Amber 7, where the code did not attempt to fix
such problems.
The test suite for antechamber has a number of examples of using it -- go
through those to see if that helps.
....dac
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Received on Mon Oct 18 2004 - 21:53:00 PDT
