AMBER: problem of calculate the charge

From: ping jiang <>
Date: Tue, 27 Dec 2005 16:47:16 -0800 (PST)

Dear Amber Users,

I am struggling with assigning the charge for the
atoms in the molecule.
Here I attached the PDB file for the undecyl-ala-Cleu
(charge: -1)molecule that I built.

Then I use antechamber to generate the charge (AM1-bcc
method)by using:
$AMBERHOME/exe/antechamber -i UAL.pdb -fi pdb -o
UAL.prepin -fo prepi -c bcc -nc -1 -s 2
$AMBERHOME/exe/parmchk -i UAL.prepin -f prepi -o

$AMBERHOME/exe/xleap -s -f
source leaprc.gaff
loadamberprep UAL.prepin
loadamberparams UAL.frcmod
loadoff UAL.lib
edit UAL

If we checked the "edit selected atoms", you can see
the undecyl part, the atom charge is Zero.

So I am just wondering how to use the antecharmer
(bcc) to get the correct charge.....
Thank you very much


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Received on Wed Jan 04 2006 - 18:17:00 PST
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