AMBER Archive (2007)

Subject: RE: AMBER: Polarizable Force Field: Ligand Parameterization et al.

From: Yong Duan (duan_at_ucdavis.edu)
Date: Thu Oct 25 2007 - 12:02:55 CDT

Dear Horn:

There are two versions of ff02, ff02r0 and ff02r1. The ff02r0 is the
original ff02 which was not fully calibrated and the main chain torsions
were not well-refined. The ff02r1 is the version after modifications of the
main chain torsion parameters by Wang et al, 2006, JCC 27(6), 781-790. This
modification was intended to improve the main chain torsion parameters. This
does not really affect typical protein simulations as it was demonstrated
that protein structures were reasonably well-maintained (with RMSD
maintained at the level comparable to other ff at the time). However, if you
have a protein with flexible loops or if you want to use it for
protein/peptide folding simulations, you should use ff02r1. You can read the
paper for detail. My suggestion is to use ff02r1 (for both obvious selfish
and practical reasons :) ).

The ff02r1 refinement was done in POL3. However, simulations on proteins
with TIP3P were seen to give similar results. TIP3P is a non-polarizable
model (or, shall I say a model already take into account the polarization).
So, you need to make sure its polarizability is set to 0.00.

Piotr (pcieplak_at_burnham.org) should have the code to do the iterative
fitting. You should contact him directly. Hopefully, it will be released as
part of AMBER tools.

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Anselm Horn
Sent: Thursday, October 25, 2007 2:00 AM
To: amber_at_scripps.edu
Subject: AMBER: Polarizable Force Field: Ligand Parameterization et al.

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

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

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