Subject: SUMMARY: Cahrge and Force Field Parametrization

From: Giuseppe Ermondi <[email-masked]>
Date: Mon, 22 Apr 2002 10:46:33 +0200

Hi CCL,

first of all I would like to thank CCL and the person who wrote me very
interesting
answers to my question.

I apologize with Jerome because I did not forward him the messages but I
hope that
this summary was usefull!

Thank to David, I think that the references that you
suggested me is sufficiente for my proposal.

Thanks to Sergio, I think that the reference that you named was:

Automatic parameterization of force field by systematic search and
genetic algorithms
Wang JM, Kollman PA
JOURNAL OF COMPUTATIONAL CHEMISTRY
22 (12): 1219-1228 SEP 2001

Finally thank to Vlad who suggested me a good web site with usefull
information.

Now the summary!

Best  regards,

Giuseppe

============================================================
Original question:
-----------------

Hi CCL,

I am working with Autodock and GROMACS and I am looking for
articles, reviews or other material regarding two subjects:

1) how can evaluate charge distribution for molecules or groups like
heme
in order to obtain reasonable charges (coherent with "classical" sets
like
Amber or Kollman charges)? Are there any compilations of charges for
uncommon
groups?

2) how can obtain reasonable parametrization for the same groups? Are
there
databases available for the more usefull programs?

Thank you

Regards

Giuseppe Ermondi

================================================================
================================================================
Jerome wrote:
--------------
Hi Giuseppe

I would appreciate if you could forward me answers you get on your
question.
CHARMM parameters and topology for for Ferrous (Fe2+) heme  can be found
at
the following URL:

http://www.pharmacy.umaryland.edu/faculty/amackere/research.html

look at:

par_all27_prot_lipid.inp
top_all27_prot_lipid.inp

I am looking for parameters for Ferric (Fe3+) heme for use with CHARMM.
If
you ever have information about that, I'd be glad to know...

Ciao,
Jerome

----------------------------------------------------------
Jerome Baudry, Ph.D.
Computational Research Scientist,
Research Coordinator
150 Noyes Lab.

Computer Applications & Network Services
School of Chemical Sciences
University of Illinois at Urbana-Champaign
505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801

Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3210; E-mail:
[email-masked]
============================================================
David wrote:
-------------

Giuseppe,

For groups like heme, and other common cofactors, it is most likely that

complete parameters exist - I know that heme is part of the standard
CHARMM protein parameter sets, and I expect that AMBER parameters exist
for it as well.  I'm not sure where to look for these, but if you look
around on the AMBER site: http://www.amber.ucsf.edu/amber/, you should
be able to find some direction.  For less common molecules, and
virtually
all drugs, you'll most likely have to come up with your own charges -
and
possibly other parameters.

Associated with the AMBER package is a program RESP - which I believe
can
be obtained separately and for free - which fits partial atomic charges
to an electrostatic potential obtained from QM calculations.  This is, I

believe, the method of choice for obtaining new charges for use in
AMBER.
I've appended BibTex entries for the two papers describing RESP, and a
few links you might like to check out are
http://www.amber.ucsf.edu/amber/charges.txt
, which is a describing of the charge fitting philosophy of the Kollman
group written by Wendy Cornell, and
http://www.amber.ucsf.edu/amber/Questions/resp.html
, which has some FAQs about RESP. Of course there are many other methods

for obtaining charges, some based of fitting the QM ESP, others based on

empirical methods, but I focussed on RESP here since you seem to be
using
the Kollman group force fields.  If you want more info about some of the

other methods, just let me know and I'd be glad to send you a bigger
list
of references.

@Article{resp1,
  author =       {Bayly, C. I. and Cieplak, P. and Cornell, W. D. and
Kollman, P. A.},
  title =        {A well-behaved electrostatic potential based method
using
charge restraints for determining atom-centered charges:  The {RESP}
model},
  journal =      jpc,
  year =         1993,
  volume =       97,
  pages =        {10269-10280},
  group =        {Kollman}
}

@Article{resp2,
  author =       {Cornell, W. D. and Cieplak, P. and Bayly, C. I. and
Kollman, P. A.},
  title =        {Application of {RESP} charges to calculate
conformational
energies, hydrogen bond energies, and free energies of solvation},
  journal =      jacs,
  year =         1993,
  volume =       115,
  pages =        {9620},
  group =        {Kollman}
}

Hope this helps!

David

--
-------------------------------------------
David F. Green
Department of Chemistry
Massachusetts Institute of Technology
77 Massachusetts Ave., Rm. 6-133
Cambridge, MA 01239
Phone: 617-258-6229
Fax:   617-253-7030
Email: [email-masked]
-------------------------------------------
======================================================
Vlad wrote:
------------

Take a look at the AMBER data base on the web...As far as I remember
there are parameters there for heme.
vlad

=======================================================
Sergio wrote,
-------------

Dear Giuseppe,

    The best way to obtain relaible charges is to use ESP charges (MK or

CHELPG) calculated by  quantum mechanical method (HF/6-31G(d) for
example).
For AMBER force field the best is to calculate charges by RESP method.n
There some programs to parametrize stretchings,  bendings and torsional
terms in a force field. I use PAPQMD developed by F.J. Luque, M. Orozco
and
C. Aleman, in Barcelona (http://www.bq.ub.es/recmol/soft.html), but in
J.
Comp. Chem., , 2001 there is a paper from Kollman that presents a new
method
for parameterization (sorry I don't find it ).

        Hope this help,

                    Sergio

    ==============================================================
Sergio Emanuel Galembeck
Assistant Professor in Physical Chemistry
Laboratorio de Modelagem Molecular
Departamento de Quimica
Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto
Universidade de Sao Paulo
Av Bandeirantes, 3900
Ribeirao Preto, SP
Brasil

phone: +55-16-602-37-65
fax: +55-16-633-81-51
e-mail: [email-masked]
==============================================================

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