AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: David A. Case (
Date: Fri Sep 08 2006 - 20:53:18 CDT

On Fri, Sep 08, 2006, Fenghui Fan wrote:

> My cAMP PDB file is:
> After I check, I think the PDB file is correct.

You are missing hydrogens at C2, C8, C1', C2', C3', C4' and C5'. Also, since
your ligand has a net charge, you have to tell antechamber that as well.
You might want to study the nucleotide residues in the standard amber library,
or look at $AMBERHOME/test/antechamber/guanine, in order to get a better
feeling for what antehcamber needs as input.


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