[AMBER] antechamber/gasteiger problem with FMN

From: Eric Pettersen <pett.cgl.ucsf.edu>
Date: Tue, 22 Jun 2010 13:08:46 -0700

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 Pettersen
                         UCSF Computer Graphics Lab

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Received on Tue Jun 22 2010 - 13:30:05 PDT
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