Dear Knut,
Acetyl-CoA is already parameterized... go to
http://q4md-forcefieldtools.org/REDDB/index.php
You should be able to find the fragments and piece it together.
It is not worth your effort to redo what has already been parameterized
with multiple orientation/multiple conformation methods.
Dean--
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
On 2/12/11 4:19 PM, "David Case" <dacase.rci.rutgers.edu> 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 - 12:30:06 PST
