AMBER Archive (2009)

Subject: [AMBER] How to take into account the charge in GAFF parameterization

From: Workalemhu Berhanu (wberhanu_at_mail.ucf.edu)
Date: Thu May 28 2009 - 18:22:07 CDT

Dear all
Hi
I have an organic molecule which has a charge of +1. I am new to amber
and I do not know where and how I could put the charge in the command
line below which is found in the TUTORIAL 4 –(Antechamber to Create
Leap Input Files ).
$AMBERHOME/exe/antechamber -i filename.pdb -fi pdb -o filename.mol2 -fo
mol2 -c bcc -s 2
I thank you very much for your help

With regards
Workalemahu

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