AMBER: Polarizable Force Field: Ligand Parameterization et al.

From: Anselm Horn <>
Date: Thu, 25 Oct 2007 11:00:03 +0200

Dear all,

I have some questions about the use and extension of the polarizable
force field FF02 and would appreciate any helpful comment (especially
because the manual says that there is still a complete force field
description and its validation missing).

(a) When in sander input file IPOL=1, is the polarizable force field
ansatz then used for all entities (atoms/molecules) during the MD? In
particular, is the polarization energy computed also for ligands or
residiues that were parameterized for a non-polarizable force field
(e.g. TIP3P-water or FF99-parameterized phosphorylated amino acids)?

(b) What is the preferred water model for an FF02 calculation? Of
course, POL3 seems obvious, but has anyone tried out the others?

(c) Is there a program/script that may be used to do the iterative
charge fitting including the self polarization as described in the
original Cieplak-Caldwell-Kollman-paper of 2001, or is there a hidden
feature in antechamber?

(d) Has anyone successfully parameterized an organic ligand in FF02?

Many thanks in advance!

Best regards,

Anselm Horn

Institut f. Biochemie
Friedrich-Alexander-Universitaet Erlangen-Nuernberg

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Received on Sun Oct 28 2007 - 06:07:20 PDT
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