[AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type.

From: Denny Bromley <dbromley.u.washington.edu>
Date: Thu, 11 Mar 2010 20:33:05 -0800

Hi All,


So, I'm assuming I'm doing something wrong here. I'm comparing antechamber
parameters against our current parameter library. I ran all twenty amino
acids through antechamber as a sort of control to do a 1:1 comparison of
parameter values. Upon close inspection, all of my carbons are of atom type
'c3' which is listed in the GAFF documentation as an sp3 carbon which
clearly can't be the case as there are plenty of ring systems and =O systems
in the twenty amino acids. Obviously I'm doing something wrong - any ideas?



My amino acid PDB files were from the Avogadro fragment library and exported
via Avogadro into the PDB format.

Antechamber installed and compiled just fine, including all the test cases
(on windows 7under cygwin as admin.)

Command line was as in the tutorial: "antechamber -i foo.pdb - fi pdb -o
foo.mol2 -fo mol2 -c bcc -s 2"


FWIW, benzofuran from the same Avogadro fragment library ends up in the same
boat with all carbons as 'c3' type.







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Received on Thu Mar 11 2010 - 21:00:02 PST
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