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.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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Anselm Horn
Sent: Thursday, October 25, 2007 2:00 AM
To: amber.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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Received on Sun Oct 28 2007 - 06:07:25 PDT
