AMBER Archive (2004)

Subject: Re: AMBER: AM1-BCC charges

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Tue Oct 26 2004 - 20:29:02 CDT

Xin,

try to use pdb coordinates extracted from g98.out. You can obtain them with:
antechamber -fi gout -i g98.out -fo pdb -o g98.pdb

I think you will get the same am1-bcc charges with this pdb file as with
direct usage of the g98.out file as input for the charge calculation.

I.e. I think that only the coordinates of the g98.out file are used, not
any other information.

So, AM1BCC is meant to get charges reproducing the electrostatic surface
potential without the need to actually calculate it.

If you want to use the electrostatic surface potential you can use the
resp modul.

Best regards,
Oliver

Xin Hu wrote:
> Dear Amber user,
> I used the antechamber to get the AM1-BCC charges of ligand directly (antechamber
> -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc). I wonder what's the difference
> if using the Gaussian to compute the electron distribution first, and then fit
> the AM1-BCC using antechamber? (antechamber -i g98.out -fi gout -o lig.mol2 -fo
> mol2 -c bcc)
>
> Thank you very much for your help.
>
> Xin
>
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-- 
________________________________________________________________

Oliver Hucke, Dr.
Biomolecular Structure Center   Health Sciences Building - K418C
Dept. of Biochemistry           1959 NE Pacific St.
University of Washington        phone: (206) 685 7046
Box 357742                      fax  : (206) 685 7002
Seattle, WA 98195-7742          email: ohucke_at_u.washington.edu
________________________________________________________________

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