Summary for HEME parameters



 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 <kris at.at bionmr1.rug.ac.be>
 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             (Kris.Boulez at.at rug.ac.be)
 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: aholder at.at vax1.umkc.edu
 > 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:  acklin at.at chbs.ciba.com
 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. case at.at cgl.ucsf.edu
 Mrigank
 ----
 Mrigank                           \/Phone  +91 172 49057
 Institute of Microbial Technology /\Email:  mrigank at.at imtech.ernet.in
 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: MARTIN%cmda at.at randb.abbott.com
 =====================================================================
 [5]
 From: Rick Loncharich <LONCHARICH_RICHARD_J at.at Lilly.com>
 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" <setlik at.at acsu.buffalo.edu>
         Rick Ornstein's email is RL_Ornstein at.at ccmail.pnl.gov.  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 <wiesiek at.at phys.uni.torun.pl>
 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: wiesiek at.at phys.uni.torun.pl (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: REISSNER at.at pembvax1.pembroke.edu
 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
 reissner at.at pembvax1.pembroke.edu     vox: (910)521-6425    fax:
 (910)521-6649
 =========================================================================
 [9]
 From: Bersuker <cmao771 at.at charon.cc.utexas.edu>
 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 <HMARQUES at.at AURUM.CHEM.WITS.AC.ZA>
 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 <d3h155 at.at monod.pnl.gov>
   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
   d3h155 at.at monod.pnl.gov
   (509) 375-2116
 =======================================================================
 [11]
 From helms at.at EMBL-Heidelberg.DE
 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: helms at.at embl-heidelberg.de
 =======================================================================
 [12]
 From arne at.at hodgkin.mbi.ucla.edu
 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 charmm-bbs at.at emperor.harvard.edu (bulletin board) for mor info
 or brbooks at.at helix.nih.gov (B. Brooks) or alex at.at mmiris.ab.umd.edu
 A.McKerrel Jr.
 (developer of par22)
 arne
 ======================================================================
 [13]
 From: Joan_Josep Lozano Salvatella <lozano at.at far.ub.es>
 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 ross at.at cgl.ucsf.EDU
 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 (case at.at scripps.edu) 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 arne at.at hodgkin.mbi.ucla.edu
 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 charmm-bbs at.at emperor.harvard.edu (bulletin board) for mor info
 or brbooks at.at helix.nih.gov (B. Brooks) or alex at.at mmiris.ab.umd.edu
 A.McKerrel Jr.
 (developer of par22)
 arne
 =======================================================================
 [16]
 From: David Case <case at.at scripps.edu>
 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: case at.at scripps.edu
 Dept. of Molecular Biology, MB1    |  bitnet: case%scripps.edu at.at sdsc
 The Scripps Research Institute     |  fax:   619-554-3789
 10666 N. Torrey Pines Rd.          |  phone: 619-554-9768
 La Jolla CA 92037  USA             |
 =====================================================================