Re: [AMBER] parametrization of acetyl-coa using antechamber

From: case <>
Date: Mon, 14 Feb 2011 12:30:44 -0500

On Sun, Feb 13, 2011, Knut Jørgen Bjuland wrote:
> I used reduce to add hydrogen bond, but I failed to described it. Having
> said that I also ran acdoctor on the same pdb file. As a matter of fact
> I am now sending along the pdb files and the log files from acdoctor. It
> appears that there is a small distance between certain atom in the pdb file.

The CONECT records in your pdb file are very strange, and probably incorrect.
It might be simplest to strip those out of the pdb file, and see if that


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Received on Mon Feb 14 2011 - 10:00:02 PST
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