Re: [AMBER] Charge parameters in GAFF

From: Stefan Menzel <>
Date: Tue, 09 Jun 2020 10:14:04 +0200

Dear Lorenzo,

Thank you a lot!

Will the quality of the charges be different if the input to antechamber is a .mol2 file instead of a .pdb file?
As far as I understand, a .pdb file is only a coordinate file, whereas a .mol2 file also contains bond information.

Best Regards,

Am Dienstag, Juni 09, 2020 08:35 CEST, schrieb Lorenzo Gontrani <>:
 Dear Stefan, the charges are normally calculated using ab initio
calculations for the ligands (using RESP, CHelpG etc) or semiempirical, for
too big systems they can be estimated with methods like Gasteiger-Marsili
(provided by antechamber)

Hope this helps
Lorenzo G.

Il mar 9 giu 2020, 07:52 Stefan Menzel <> ha

> Dear Amber Mailing List,
> Where can I find the charge parameters for the Generalized Amber Force
> Field?
> I only have AmberTools and the gaff.dat file.
> Thank you & Best Regards,
> Stefan
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Received on Tue Jun 09 2020 - 01:30:03 PDT
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