Trying to add Gasteiger charges to flavin mononucleotide (mol2 file
attached; based on PDB entry 3fx2) using Antechamber from AmberTools
1.4 with bugfix 1 applied as follows:
antechamber -i ante.in.mol2 -fi mol2 -o ante.out.mol2 -fo mol2 -c gas -
nc -1 -j 5 -s 2
produces the following error:
The net charge of the molecule (-1) does not equal to the total charge
(0.00 ) based on Gasteiger atom type, exit
With the protonation state given in the mol2 file, the net charge
should clearly be -1. Apparently there is something wrong with the
"Gasteiger atom types" that antechamber is producing.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
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Received on Tue Jun 22 2010 - 13:30:05 PDT
