From qftramos@usc.es Fri Dec 23 04:30:25 1994 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.6.9/930601.1506) id DAA19053; Fri, 23 Dec 1994 03:53:34 -0500 Received: by uscmail.usc.es (5.67b/1.34) id AA18375; Fri, 23 Dec 1994 09:55:44 +0100 Date: Fri, 23 Dec 1994 09:55:44 +0100 From: qftramos@usc.es (Antonio Fernandez Ramos) Message-Id: <199412230855.AA18375@uscmail.usc.es> To: chemistry@ccl.net Subject: POLYRATE questions Dear netters: I am beginning to use POLYRATE in intramolecular proton transfer in symmetric wells,i.e.,malonaldehide and similar systems. I have decided to use a numerical surface with the POTENTIAL=unit30 option,and I have got some doubts: -How could I extrapole the MEP after reactants or products? -How many points are necessary to obtain right results? -The effect of tunneling in the malonaldehyde is very important, Do I need to use large curvature tunneling to obtain the rate constant and evaluate the kinetic isotope effect in these molecules to obtain good results? -Do I need to know how large the reaction coordinate is to make these calculations? Thanks and best regards. Antonio F. Ramos e-mail:qftramos@usc.es From zoellner@cacao.issecc.fi.cnr.it Fri Dec 23 06:30:26 1994 Received: from pc1.issecc.fi.cnr.it for zoellner@cacao.issecc.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id FAA19511; Fri, 23 Dec 1994 05:54:10 -0500 From: Message-Id: <199412231054.FAA19511@www.ccl.net> To: chemistry@ccl.net Subject: Dipole moments and charged species Date: Fri Dec 23 10:55:01 1994 Greetings from Firenze! One of my students has asked me a question (really a group of related questions) which has arisen before in my research group, and to which I do not have truly satisfactory answers. Now that I have access to the CCL, I decided to ask it/them of all of you CCL subscribers: 1) Can a species already carrying a charge have a dipole moment as well? 1a) If so, can such a moment (multipole, perhaps?) be calculated in any satisfactory way? 1b) If not, why not? 2) When calculations are carried out on charged species, the result often includes a value for "dipole" moment, yet these values are unreliable. If the "origin" of the ion is changed, with no other changes in bonds, angles, or torsions, the value for the "dipole" can also change. If the origin for charged species was defined as always being at the center of mass, would the resulting value for dipole moment have any validity? 3) Can charge be treated as an "additive" property so that a dipole moment could be calculated for the uncharged species as the structure determined for the charged species, and then adding the extra charge after that? (In other words, making the dipole moment of the charged species the same as the dipole moment for the hypothetical uncharged species?) I have only some general references from the 1930's concerning the determination of quadrupole moments, but nothing more current than that. My apologies to all if these questions seem naive...my students often stump me with seemingly simple ideas which are outside of my areas of so-called "expertise". Thanks in advance for your responses. I shall post a summary of replies. Bob Zoellner zoellner@nauvax.ucc.nau.edu zoellner@cacao.issecc.fi.cnr.it Robert W. Zoellner, Ph.D.; Associate Professor of Chemistry [currently on sabbatical from Northern Arizona University] ISSECC-CNR; Via Jacopo Nardi, 39; 50132 Firenze; Italy Office telephone: (39-55) 24.59.90 FAX: (39-55) 24.78.366 Home address: Via di Bellariva, 9; 50136 Firenze; Italy Home telephone: (39-55) 67.77.98 From erens@chem.rug.nl Fri Dec 23 10:30:31 1994 Received: from rugch4.chem.rug.nl for erens@chem.rug.nl by www.ccl.net (8.6.9/930601.1506) id KAA22368; Fri, 23 Dec 1994 10:13:09 -0500 Message-Id: <199412231513.KAA22368@www.ccl.net> Received: from rugch5.chem.rug.nl by rugch4.chem.rug.nl with SMTP (1.37.109.4/16.2) id AA29950; Fri, 23 Dec 94 16:13:01 +0100 Received: by rugch5.chem.rug.nl (1.37.109.4/16.2) id AA02678; Fri, 23 Dec 94 16:11:59 +0100 From: "R.L.W.M. Erens" Subject: DGAUSS and dissociating LiF orbital-mix To: chemistry@ccl.net Date: Fri, 23 Dec 94 16:11:59 MET Mailer: Elm [revision: 70.85] Dear Netters, I have a question regarding the resulting vectors and energy of the input shown below for the DFT-based program DGAUSS (version 2.3). In order to get familiar with this program, I wanted to calculate the energy of a LiF molecule at various distances interatomic separations. I calculated the sum of the energies of the two atoms to be about -106.45 a.u. At large interatomic separation, I could approach this sum by using OCCUP 2 7 5 4 0 1.0 1.0 1.0 1.0 i.e. each atom having an open shell electron with spin alpha The resulting 7 alpha MO's are of pure F(s) Li(s) F(s) 3*F(p) and Li(s) AO character. The beta orbitals are pure as well. Using the MO's of this job as startvectors I also could approach the sum with OCCUP 2 7 7 1 2 0.0 0.0 1.0 i.e. Li is to have a beta electron in stead of an alpha open shell electron Again the resulting MO's have purely atomic character. However, when not using this explicit occupation scheme but the input below, (the startvectors as the former calculation) I find an energy of -106.48 a.u. which is BELOW the sum. Also some of the MO's contain coefficients of both Li(s) AO's AND F(p) AO's, which for such large distances is not expected. Another interesting point is that some of the resulting occupied MO's have a higher 1-electron energy than one of the empty MO's. Not using the startvectors leads to a spinrestricted solution, again lower in energy, again mixing of AO's from different atoms. Has anyone met such a case before or some sort of explanation for the lower energy? And why is the aufbau principle not used, although the manual says the program does? Any comments will be greatly appreciated. Thank you very much, Roger Erens erens@chem.rug.nl ##### COPY DATA FILES TO EXECUTION DIRECTORY cp /usr/local/unichem/2.3/dgauss_basis/* . cp /$HOME/DScfvecLiFtrip ./DScfvec ##### GENERATE DGAUSS INPUT DECK cat >dgauss.in < Sender: Weifan Zheng Reply-To: Weifan Zheng Subject: Summary for HEME parameters To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII 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 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@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@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@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@cgl.ucsf.edu Mrigank ---- Mrigank \/Phone +91 172 49057 Institute of Microbial Technology /\Email: mrigank@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@randb.abbott.com ===================================================================== [5] From: Rick Loncharich 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" Rick Ornstein's email is RL_Ornstein@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 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@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@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@pembvax1.pembroke.edu vox: (910)521-6425 fax: (910)521-6649 ========================================================================= [9] From: Bersuker 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 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 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@monod.pnl.gov (509) 375-2116 ======================================================================= [11] >From helms@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@embl-heidelberg.de ======================================================================= [12] >From arne@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@emperor.harvard.edu (bulletin board) for mor info or brbooks@helix.nih.gov (B. Brooks) or alex@mmiris.ab.umd.edu A.McKerrel Jr. (developer of par22) arne ====================================================================== [13] From: Joan_Josep Lozano Salvatella 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@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@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@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@emperor.harvard.edu (bulletin board) for mor info or brbooks@helix.nih.gov (B. Brooks) or alex@mmiris.ab.umd.edu A.McKerrel Jr. (developer of par22) arne ======================================================================= [16] From: David Case 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@scripps.edu 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 | =====================================================================