Subject: Summary for HEME parameters

From: Weifan Zheng <[email-masked]>
Date: Fri, 23 Dec 1994 13:04:45 -0500 (EST)

Dear netters,

I posted a question about HEME parameters a while ago. Since there is a 
general interest, I'd like to summarize some of the answers here.

Thanks to all those who provided the following answers

Weifan

Lab for Molecular Modeling
School of Pharmacy
UNC-Chapel Hill
NC 27599-7360

Original question:
 
> 
>    (1) any parameters ( Molecular Mechanics force field parameters ) for HEME
>        group;
>    (2) what is the suitable way to calculate atomic charges of the  
>        atoms of HEME group including Fe.

Answers:

==========================================================================
[1]

From: Kris Boulez <[email-masked]>

In Insight (Biosym Inc.) parameters for the heme group for their cvff
forcefield are included in the gifts directory (3rd party, non supported,
but work OK). ...

Kris,
---
Kris Boulez             ([email-masked])
Biomolecular NMR unit
University of Ghent, Belgium

==========================================================================
[2]

1. you can try to handle iron complexes with universal forcefields in
   cerius2, for instance, or as you work with one kind of complex you can
   adapt force field like amber or others by introducing parameters form x-ray
   or ab initio calculation.

2. hamiltonians for iron are included in some semi empirical programs. There
   are three of them, as far as I know; Zindo (don't know the source)
   Ampac (Semichem, see address)
   Mndo/d (Prof. W. Thiel, University
   of
   Zuerich, lab for org. chem)

semichem:

>                     DR. ANDREW HOLDER
>                    President, Semichem
>
> Semichem, Inc.            ||  Internet Addr: [email-masked]
> 7128 Summit               ||  Phone Number:  (913) 268-3271
> Shawnee, KS,  66216       ||  FAX Number:    (913) 268-3445

I am trying to get some more reliable results using GaussianDFT.

hope this helps

Pierre Acklin

-- 
____________________________________________________________________

Dr. Pierre Acklin                       email:  [email-masked]

smail:  Ciba-Geigy AG                   tel:    ++41 61 696 23 62
        K-136.P.13                      tel:    ++41 61 696 23 75
        CH-4002 Basel                   fax:    ++41 61 696 27 61
_____________________________________________________________________   

=====================================================================
[3]

Data set with Amber 4.0 contains all these parametes. Dave Case can definitly
help you. [email-masked]

Mrigank
----
Mrigank                           \/Phone  +91 172 49057     
Institute of Microbial Technology /\Email:  [email-masked]
Sector 39A,                       \/FAX: +91 172 40958, +91 172 28032          
Chandigarh 160 014 India.         /\ 
==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+
-- When I feed the poor, they call me saint. When I ask why the poors do
   not have food, they call me communist - Archbishop Camaran

=====================================================================
[4]

You should get a response from someone at Biosym since Peter Goodford
used Discover on hemoglobin a while back.

Yvonne Martin
Abbott Laboratories
From: [email-masked]

=====================================================================
[5]

From: Rick Loncharich <[email-masked]>
The CHARMM (Harvard)/CHARMm (MSI) program has parameters for the 
heme group.  We published some corrections to the heme topology file
because the minimized structure came out saddle shaped, see 
J. Mol. Biol. 215, 439-455, 1990. 
Rick

=====================================================================
[6]
From: "Robert F. Setlik" <[email-masked]>

        Rick Ornstein's email is [email-masked].  The parameters
used by his group for the P450 heme are derived from standard Discover 
params, however I know that he has spent a lot of effort in deriving new
charges for the heme.

Cheers,

Rob Setlik

_______________________________________________________________

Robert F. Setlik
Biophysics Department,
Roswell Park Cancer Institute,
Buffalo, NY
14263.
CCC 218

Phone (716) 845-3048 (lab)
_______________________________________________________________
=================================================================
[7]

From: Wieslaw Nowak <[email-masked]>

Dr. Wieslaw Nowak
Molecular Biophysics Group
Institute of Physics
N.Copernicus University
ul. Grudziadzka 5
PL-87-100 Torun, Poland

tel. (48-56) 210-65 ext. 213, 216
fax. (48-56)  253-97
telex 055412 umk pl

e-mail: [email-masked] (internet)
-----------------------------------------------------------
I noticed your recent question on heme group parameters
suitable for modeling of P-450. I know (so far) only two
programs which have parameters for FE+2 used in modeling of 
heme proteins:
- CHARMM (which you probably know, commercial version is distributed
by MSI, there is also an academic version)
- MOIL ( a public domain, relatively new MD program, it is available
via anonymous ftp from 128.248.186.70, directory dist).

========================================================================
[8]
 
From: [email-masked]

Jan Hermans' group, right at UNCCH albeit
in Biochemistry&Biophysics, has done this.
The question as to the charge of the metal
ion presumably relates to charge redistribution
within the ligand complex; I wonder to what
extent EPR on the one hand, and ESCA/PES on the
other, shed light on this as an experimental
problem.

John

John Reissner         Pembroke State University     Pembroke NC  28372  USA
[email-masked]     vox: (910)521-6425    fax: (910)521-6649

=========================================================================
[9]
From: Bersuker <[email-masked]>

Concerning your problem, may I recommend you have a look into our paper 8
about modeling transition metal systems...

Regards
Isaac

===========================================================================
[10]

From: Helder Marques <[email-masked]>

We have published an augmentation of the MM2 force field for 
porphyrins: JACS, 1992, 112, 7218.

A further refinement of the force field for Fe(III) poprhyrins with 
imidazoles or pyridines as axial ligands is in press in JACS and 
should appear in the next few months:  Munro, Marques, Debrunner, 
Mohanrao and Scheidt, "Structural and Molecular Mechanics Studies in 
highly ruffled low-spin [porphinato]iron(III) complexes."

We have just submitted a manuscript giving the details of the force 
field for the porphyrin ring itself to J. Chem. Soc., Faraday 
Transactions.  If you are interested, let me know and I'll mail you a 
copy of the manuscript.

Best wishes

Helder Marques 
------------------------------------------------------------
Prof. Helder M. Marques, Department of Chemistry
University of the Witwatersrand, P.O. Wits
2050 Johannesburg,
South Africa
Fax: Int + 27 + 11 + 339-7967
------------------------------------------------------------

=======================================================================
[11]

Date: Thu, 01 Dec 1994 17:48:09 -0800
From: Mark Paulsen <[email-masked]>

  I was reading the computational chemistry list today and noticed 
your request for heme parameters for modeling P450.  I may be able 
to point you in the right direction.  What modeling package will you
be using?  There are at least two group I know of that are using AMBER 
to do P450 studies, Jeff Jones and his coworkers at the University of 
Rochester and Gilda Loew and her coworkers at MRI.  I am sorry but I don't
have e-mail addresses for either of them.  But if you contact them 
directly, they may be willing to share their parameters.  

 If you are using BIOSYM software to do the modeling, our work may be of 
use to you.  We have published a number of studies of P450-substrate complexes
using a forcefield that we are developing in house.

  If you are using some other package you will need to adapt one of the 
published forcefields.

  Please let me know if I can be of any additional help

  Mark Paulsen
  Environmental Molecular Sciences Laboratory
  Pacific Northwest Laboratory
  [email-masked]
  (509) 375-2116

=======================================================================
[11]

>From [email-masked]

I am aware of the following work which has been published concerning
studies on cytochrome P450 by molecular mechanics/dynamics methods:

AMBER forcefield
----------------
G. Loew's group:
JACS 113,2736-2743 (1991)
JACS 114,6987-6993 (1992)
JACS 115,8775-8779 (1993)

J.Jones,W.F.Trager,T.J.Carlson
JACS 115,381-387 (1993)

Discover forcefield
-------------------
Rick Ornstein's group:
J.Biomol.Struct.Dyn. 9,187-203 (1991)
Proteins 11,184-204 (1991)
J.Comp.Aid.Mol.Des.6,449-460 (1992)
Proteins 13,26-37 (1992)
Biochem.Biophys.Res.Comm. 189,488-495 (1992)
J.Comp.Chem. 14,541-548 (1993)
Prot.Eng. 6,359-365 (1993)
Prot.Science 2,357-365 (1993)

Volkhard Helms
--
Volkhard Helms
European Molecular Biology Laboratory
Meyerhofstr.1
69012 Heidelberg, Germany
Tel. +49 - 6221 - 387255
e-mail: [email-masked]

=======================================================================
[12]

>From [email-masked]

Heme is parameterized in the charmm force-field
(param19, param20 (not recomended) and probably the bast in par22)
I think MSI distributes a par21 and maybee par23 also
that include heme.

Contact [email-masked] (bulletin board) for mor info
or [email-masked] (B. Brooks) or [email-masked] A.McKerrel Jr.
(developer of par22)

arne

======================================================================
[13]

From: Joan_Josep Lozano Salvatella <[email-masked]>

Try AMBER for make molecular dynamics of Hemo proteins (See G.Loew ian
International Journal of Quantum Chemistry ,Biologia symposia...
use a reference of G.Loew)

I also work with hemoproteins P450IA2...it's difficult!

Respect charges...

Use ARGUS (INDO/s)
Or recently AMPAC with Fe parameters .
Also LAMB1MZ (I THIK^H) ab initio basis ECP aproximations...

Juanjo Lozano

=====================================================================
[14]

>From [email-masked]

Did you ever hear from Dave Case? We have some heme parameters
of his in the Amber release. His notes on them are:

 ...Files useful for manipulating heme proteins.  These include
 prep input for united atom and all atom heme groups (heme_uni.in
 and heme_all.in) along with frcmod files for use with parm.
 Use these carefully, since they are not part of the "standard"
 AMBER distribution.  Contact David Case ([email-masked]) if
 you have questions about how these were generated.  The heavy
 atom names for the heme ring follow Brookhaven ideas, but the
 protons are named according to a local, nmr-based convention.
 For historical reasons, the united atom parameters are set up for
 a deoxy heme, whereas the all-atom frcmod file is set up for a
 ligated heme; you will want to carefully study these before
 using them.

If you are using Amber, you would only need to worry about how good
the params are; if some other program, you'd also need to figure
out the best way to translate them.

Let me know is you want them (charge on Fe is included).

Bill Ross

===================================================================
[15]

>From [email-masked]

Heme is parameterized in the charmm force-field
(param19, param20 (not recomended) and probably the bast in par22)
I think MSI distributes a par21 and maybee par23 also
that include heme.
 
Contact [email-masked] (bulletin board) for mor info

or [email-masked] (B. Brooks) or [email-masked] A.McKerrel Jr.
(developer of par22)

arne

=======================================================================
[16]

From: David Case <[email-masked]>

These parameters are the the "dat" directory of the AMBER distribution
(if you have that), or you can obtain them by anonymous ftp from
ftp.scripps.edu, in file pub/case/heme.AMBERparms.tar.Z.  If you are not
an AMBER user, you will have to decipher the file format, but I think
mostly it's pretty self-explanatory.

...good luck....dave case
=====================================================================
David A. Case                      |  internet: [email-masked]
Dept. of Molecular Biology, MB1    |  bitnet: case%scripps.edu@sdsc
The Scripps Research Institute     |  fax:   619-554-3789
10666 N. Torrey Pines Rd.          |  phone: 619-554-9768
La Jolla CA 92037  USA             |
=====================================================================