Re: [AMBER] atom-type cz ???

From: Barbault Florent <florent.barbault.univ-paris-diderot.fr>
Date: Wed, 3 Mar 2010 16:59:58 +0100

Hello,

Enclosed is the pdb input file and the prep output file. I use the following
command:

antechamber -i pdb_input.pdb -fi pdb -o prep.prep -fo prepi -c bcc -rn LIG -nc
1

The global charge is +1, and if I add all atomic partial charges I find it is
correct.

Thanks
Florent Barbault




Le mercredi 3 mars 2010, case a écrit :
> On Wed, Mar 03, 2010, Barbault Florent wrote:
> > I am having trouble with the gaff force-field. I used antechamber to
> > generate, from ligand coordinates, my prep file and, when I open this
> > file, I found a carbon atom of cz type. However, this type is not
> > reported in gaff.dat file...
>
> Looks like a bug; there is a "cz" atom type defined in ATOMTYPE_GFF.DEF,
> but nothing in gaff.dat. Can you post the input pdb (or other) file you
> used?
>
> I'm forwarding this to Junmei Wang for comments.
>
> Thanks for the report...dac
>
>
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-- 
-------------------------------------------------
Dr Florent Barbault
Maitre de conferences
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/spip.php?article77
tel  : (33) 01-57-27-88-50
e-mail : florent.barbault.univ-paris-diderot.fr




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Received on Wed Mar 03 2010 - 08:30:02 PST
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