Re: AMBER: problem of calculate the charge

From: David A. Case <>
Date: Fri, 30 Dec 2005 09:58:47 -0800

On Tue, Dec 27, 2005, ping jiang wrote:
> 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
> If we checked the "edit selected atoms", you can see
> the undecyl part, the atom charge is Zero.

I cannot reproduce this problem. I used your input UAL.pdb file, and the
charges look pretty reasonable to me (not zero on the cyl part, etc.).

Can you just look at the UAL.prepin file itself to check the charges? Also,
look at the divcon or mopac output file for any clues as to what might be
going wrong. Are you getting reasonable charges on the peptide group? Which
version of Amber/antechamber are you using?

You might be having a problem because of the TER card inside the UAL.pdb file.
TER cards should only be placed between separate molecules, although I think
antechamber ignores this. Remember that antechamber really works on just
whole molecules.


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