AMBER Archive (2006)

Subject: Re: AMBER: a ligand file

From: David A. Case (case_at_scripps.edu)
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.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu