(unknown charset) Re: [AMBER] parametrization of acetyl-coa using antechamber

From: (unknown charset) Knut Jørgen Bjuland <knutjorgen1.yahoo.no>
Date: Sun, 13 Feb 2011 10:00:02 +0100

Hi


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.


Knut J

On 02/12/2011 11:19 PM, David Case wrote:
> On Feb 12, 2011, at 1:29 PM, Knut Jørgen Bjuland<knutjorgen1.yahoo.no> wrote:
>
>> Hi have installed just Ambertools 1.4 and I am working on paramerization
>> of acetyl-Coa from 3PW8.
> Make sure the input file to antechamber has all hydrogen atoms present. Most ligands from the pdb are missing these. Many programs can add them, including reduce or sleap (look for the "hbuild" command.)
>
> ...dac
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Received on Sun Feb 13 2011 - 01:30:02 PST
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