It worked, thanks a lot for your help!!
Best wishes,
Rebeca.
> From: farid.ou.edu
> To: amber.ambermd.org
> Date: Wed, 13 Feb 2013 18:56:48 +0000
> Subject: Re: [AMBER] charged molecule with antechamber
>
> 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 - 11:30:03 PST
