Re: [AMBER] Antechamber trouble with COA-acyl chain

From: case <>
Date: Wed, 13 Jul 2011 18:06:14 -0400

On Wed, Jul 13, 2011, Erin Kelly wrote:
> I've editted the original pdb with the coordinates from Dr. Case (thank you
> for this information!), there seems to be a problem with one of the
> phosphate groups

There is indeed some funny business with the geometry of the phosphate groups,
including the P-O-P angle of nearly 180 degrees. I'm inclined to attribute
this to a failure of AM1, not the computer codes themselves. This may be a
case where the automatic am1-bcc scheme is questionable, and that RESP charges
would be better. Others with more experience in this area may want to chime
in here.


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Received on Wed Jul 13 2011 - 15:30:03 PDT
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