From andrey@atp.biochem.usyd.EDU.AU Sat Oct 1 05:16:15 1994 Received: from metro.ucc.su.OZ.AU for andrey@atp.biochem.usyd.EDU.AU by www.ccl.net (8.6.9/930601.1506) id EAA12666; Sat, 1 Oct 1994 04:24:35 -0400 Received: from atp.biochem.usyd.EDU.AU by metro.ucc.su.OZ.AU with SMTP id AA28926 (5.65c/IDA-1.4.4 for ); Sat, 1 Oct 1994 18:24:33 +1000 Received: from nicePC.biochem.usyd.EDU.AU by atp.biochem.usyd.edu.au (5.0/SMI-SVR4) id AA03676; Sat, 1 Oct 94 18:18:38 EST Message-Id: <9410010818.AA03676@atp.biochem.usyd.edu.au> From: "Andrey Bliznyuk" To: chemistry@ccl.net Date: Sat, 1 Oct 1994 18:10:43 Subject: Charges Reply-To: A.Bliznyuk@biochem.usyd.edu.au Priority: normal X-Mailer: Pegasus Mail/Windows (v1.11a) Content-Length: 1126 Dear Netters, With great interest I have read the material about determination of charges for MM calculations. It seems, that people forgot to mention one more approach to the problem: fitting charges to reproduce ab-initio energy of intermolecular interactions. This method has been used in groups of Clementi and Jorgensen. The last references I have on my table are: M. Aida, G. Corongiu, E. Clementi "Ab initio force field for simulations of proteins and nucleic acids" Int. J. Quant. Chem. 1992, v.42, p.1353-1381 J. Pranata, S.G. Wierschke, W.L. Jorgensen "OPLS potential functions for nuclear bases. Relative association constants of hydrogen-bonded base pairs in chloroform" J. Am. Chem. Soc., 1991, v.113, p.2810-2819. From general point of view, this method seems more accurate than obtaining charges from EP, because it includes polarization. Unfortunately, it is computationaly more expensive and it is not clear, that it gives better results. (Once again a problem with comparing results from different force fields). Dr. Andrey Bliznyuk Department of Biochemistry University of Sydney, NSW 2006, Australia From jamejias@obelix.cica.es Sat Oct 1 08:16:17 1994 Received: from obelix.cica.es for jamejias@obelix.cica.es by www.ccl.net (8.6.9/930601.1506) id HAA13175; Sat, 1 Oct 1994 07:23:16 -0400 From: Date: Sat, 1 Oct 94 12:23:06 +0100 Received: by obelix.cica.es (5.64/X1.00) id AA12167; Sat, 1 Oct 94 12:23:06 +0100 Message-Id: <9410011123.AA12167@obelix.cica.es> To: CHEMISTRY@ccl.net Subject: Ab Initio EPR? Dear Netters Can somebody answer those questions? 1) Is it possible to predict or at least to interpret EPR spectra from ab initio quantum mechanical calulations for radicals? 2) If so, is there software to do it from the information given by standard quantum chemical calculations codes? 3) Which kind of calculation is neccesary or recommended to calculate EPR spectra? Is it enough with Hartree-Fock calculations, say UHF, or is it neccesary to go beyond Hartree-Fock wavefuncion? 4) How good is the spin density given by UHF calculations when compared to that given by EPR? Please, answer directly to me. Of course, I shall summarize for the net. Thank you in advance Jose Antonio Mejias Romero Departamento de Quimica-Fisica Universidad de Sevilla. Spain e-mail: jamejias@obelix.cica.es From Don_Gregory@msi.com Sat Oct 1 09:16:18 1994 Received: from msi.com for Don_Gregory@msi.com by www.ccl.net (8.6.9/930601.1506) id IAA13465; Sat, 1 Oct 1994 08:39:24 -0400 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA03909; Sat, 1 Oct 94 08:40:02 EDT Message-Id: <9410011240.AA03909@msi.com> Date: 1 Oct 1994 08:36:47 +0000 From: "Don Gregory" Subject: None To: "OSC Chemistry" Subject: Time:8:27 AM OFFICE MEMO None Date:10/1/94 In light of Dr. Andrey Bliznyuk's mention regarding empirical adjustments of charges to fit ab inition interaction energies: "It seems, that people forgot to mention one more approach to the problem: fitting charges to reproduce ab-initio energy of intermolecular interactions." I thought I'd expand upon, and possibly clarify the earlier notes from MSI by Dr.s Rone and Czerminsky with the following, short, description of how charges are optimized within the MSI Quanta4.0/CHARMm22 force-field. MSI's CHARMm charges are generated much as the same way as Harvard's approach, i.e. high level ab initio calculations are used to determine the ESP charges as starting points for the point charges being placed on nuclear centers. Then, a number of ab initio "interaction energies" between the solute/model and water molecules are determined, where the waters have been placed at various locations around the solute molecule. These ab initio interaction energies are then used as "observables" in adjustments of the initial charges obtained in the early stages, so that the empirical, non-bonded energies compare as best as possible, with those ab initio interaction energies. Don Gregory Mgr. Application Science Molecular Simulations Inc. (dgregory@msi.com) From ravishan@swan.wcc.wesleyan.edu Sat Oct 1 10:16:21 1994 Received: from swan.wcc.wesleyan.edu for ravishan@swan.wcc.wesleyan.edu by www.ccl.net (8.6.9/930601.1506) id JAA13743; Sat, 1 Oct 1994 09:42:10 -0400 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA16406; Sat, 1 Oct 1994 09:47:39 -0400 Date: Sat, 1 Oct 1994 09:47:39 -0400 Message-Id: <9410011347.AA16406@swan.wcc.wesleyan.edu> From: "G. Ravishanker" To: chemistry@ccl.net Subject: Water models and computational times Hi Has anyone compiled data on the computational time required for various models of water for doing MD. I know that it is a function of a lot of things, and one can estimate the time (such as the fact that a 3-center model requires 9 pair energy computations vs 4-center model requiring 16 pair energy computations). I am interested in timings from real calculations, using SPC, TIP3 and TIP4 waters with SHAKE. Thanks in advance. Ravi -- **************************************************************************** * Ganesan Ravishanker Ph: (203) 685-2104 * * Coordinator of Scientific Computing, Fax:(203) 685-2211 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06459. * **************************************************************************** From ravishan@swan.wcc.wesleyan.edu Sat Oct 1 10:30:53 1994 Received: from swan.wcc.wesleyan.edu for ravishan@swan.wcc.wesleyan.edu by www.ccl.net (8.6.9/930601.1506) id JAA13761; Sat, 1 Oct 1994 09:50:11 -0400 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA14360; Sat, 1 Oct 1994 09:55:45 -0400 Date: Sat, 1 Oct 1994 09:55:45 -0400 Message-Id: <9410011355.AA14360@swan.wcc.wesleyan.edu> From: "G. Ravishanker" To: chemistry@ccl.net Subject: Polarizable models for water Hi This question is related to all the discussion going on with the charges derived for atoms to be used in MM calculations. We are interested in exploring polarizable model for water. The literature has very interesting work from several labs in the past five years or so. The question is basically the following. The starting point for all these approaches seem to be an already existing model of water, on top of which polarizability is incorporated (either as additive or non-additive potential). As several recent messages to this list point out directly or indirectly, the charges for atoms in existing models of water were generated so as to satisfy the ab-initio energies. This implies that polarizability is already implicit in the derived charges. So, adding polarizability on top of this is likely to overestimate (or underestimate) the effects due to polarization. I would like to hear comments from others on this. Ravi -- **************************************************************************** * Ganesan Ravishanker Ph: (203) 685-2104 * * Coordinator of Scientific Computing, Fax:(203) 685-2211 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06459. * **************************************************************************** From san@mbu.iisc.ernet.in Sat Oct 1 14:16:26 1994 Received: from sangam.ncst.ernet.in for san@mbu.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id NAA15522; Sat, 1 Oct 1994 13:51:53 -0400 From: Received: from soochak.ncst.ernet.in (soochak.ncst.ernet.in [144.16.11.100]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id XAA09554 for ; Sat, 1 Oct 1994 23:21:14 +0500 Received: from nic.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by soochak.ncst.ernet.in (8.6.8.1/8.6.5) with SMTP id XAA14597 for ; Sat, 1 Oct 1994 23:20:18 +0530 Received: by nic.iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA09555; Sat, 1 Oct 94 23:25:03 EST Date: Sat, 1 Oct 94 23:25:03 EST Message-Id: <9410020425.AA09555@nic.iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA11126; 1 Oct 94 13:46:14 EST (Sat) To: vigyan!chemistry@ccl.net Subject: helical wheel plots, Hi Friends! About two-three days back i wrote to CCL asking for program to plot helical wheel diagram given the sequence of an alpha helix. One of the possible sources seems to be GCG package. However, as far as i know this package does not have a program to straightaway take the sequence and plot helical wheel. I am checking the point with GCG people. Meanwhile I have written a very simple fortran program to do my job. I generate the coordinates from an arbit point giving it rotations of 100 degrees at each successive points. These coordinates can then be visualized in any graphics program e.g. DTMM. I have no problems to send the code if anybody requires it. I thank Jie yuan, Bernard pabsch, Tom Coonor, Shoba ranganathan, Dave elrod, Alex. Tropsha for their prompt responses sandeep kumar