Perhaps, add "-nc 1" to antechamber command for +1 charge? antechamber -h for more information on the available options.
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Rebeca García Fandiño [regafan.hotmail.com]
Sent: Wednesday, February 13, 2013 12:45 PM
To: amber.ambermd.org
Subject: [AMBER] charged molecule with antechamber
Hello,
I am trying to parametrize a charged molecule (total charge = +1) using antechamber.
The problem is that although in the output file from Gaussian my charge is 1, when I do the following, I get an output with total charge 0:
$AMBERHOME/exe/espgen -i SP_out -o charges.esp
$AMBERHOME/exe/antechamber -i minimizado.mol2 -fi mol2 -o minimizado.ac -fo ac
$AMBERHOME/exe/respgen -i minimizado.ac -o minimizado.respin1 -f resp1
$AMBERHOME/exe/respgen -i minimizado.ac -o minimizado.respin2 -f resp2
$AMBERHOME/exe/resp -i minimizado.respin1 -o minimizado.respout1 -e charges.esp -t qout_1 -O
$AMBERHOME/exe/resp -i minimizado.respin2 -o minimizado.respout2 -e charges.esp -t qout_2 -q qout_1 -O
$AMBERHOME/exe/antechamber -i minimizado.ac -fi ac -o minimizado_resp.mol2 -fo mol2 -c rc -cf qout_2
In the charges column of minimizado_resp.mol2, the sum of the charges is 0, not +1.
Does anybody know which could be the problem? Any help will be very appreciated!
Best wishes,
Rebeca.
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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Received on Wed Feb 13 2013 - 11:00:04 PST
