From craig@occam.gh.wits.ac.za Thu Jan 11 01:32:34 1996 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by www.ccl.net (8.6.10/950822.1) id BAA13801; Thu, 11 Jan 1996 01:24:49 -0500 Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id IAA14978; Thu, 11 Jan 1996 08:25:01 +0200 Date: Thu, 11 Jan 1996 08:25:00 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Mehran Jalaie cc: chemistry@www.ccl.net Subject: Re: CCL:unit cell replication routine In-Reply-To: <199601101910.TAA03409@sos1.chem.iupui.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I am looking for a Fortran code that takes in crystallographic > specification of a molecule and replicates a sufrface from that. I have a "C" code program that can read crystallographic atomic data in various formats and perform symmetry operations on it, including boxing the system into a specified box of unit cells (with automatic expansion using input symmetry, and removal of redundant atoms on special positions). It also doesn't seem to suffer from the common bug I've found in most commercial fortran codes (eg. schakal and Sybyl/crysin) where two fold axes are often messed up. Sorry it's not in fortran. If you're interested, the program is called 'steric' and can be found in: ftp://hobbes.gh.wits.ac.za/pub/steric/ It is a program designed to do a large variety of other taskes, but can be used for symmetry expansion as well. See the module 'crystal.c' for the specific code. Cheers, Craig "Never make anything simple and efficient when a way can be found to make it complex and wonderful." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa tel: +27-11-716-2290 fax: +27-11-716-3826 email: craig@hobbes.gh.wits.ac.za www: http://www.gh.wits.ac.za/craig From bruno@copssg.univ-lyon1.fr Thu Jan 11 05:32:37 1996 Received: from copssg.univ-lyon1.fr for bruno@copssg.univ-lyon1.fr by www.ccl.net (8.6.10/950822.1) id FAA15146; Thu, 11 Jan 1996 05:19:23 -0500 Received: by copssg.univ-lyon1.fr (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id LAA08099; Thu, 11 Jan 1996 11:19:16 +0100 From: "Bruno Fong-Ponne" Message-Id: <9601111119.ZM8097@copssg.univ-lyon1.fr> Date: Thu, 11 Jan 1996 11:19:16 +0100 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: OPLS parameters for carbohydrates Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all, In order to do FREE ENERGY calculation I'm looking for opls parameters for cyclodextrins with trifluoroacetyl substituents. The program used is BOSS under sybyl 6.2 molecular modelling software. So all informations about the method to calculate the LENNARD-JONES parameters : epsilon and sigma used by the BOSS program are welcome. All suggestions to do such calculations with sybyl 6.2 are warmly desired. Thanks in advance for the help Bruno Fong-Ponne -- Bruno Fong-Ponne LCOPS - bat 305 Universite Claude Bernard tel (+33) 72 43 11 39 43 BD du 11 novembre 1918 fax (+33) 72 43 81 36 F-69622 Villeurbanne e-mail bruno@copssg.univ-lyon1.fr From owner-chemistry@ccl.net Thu Jan 11 07:02:38 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA16334; Thu, 11 Jan 1996 06:59:27 -0500 Received: from uscmail.usc.es for qfsaulo@usc.es by bedrock.ccl.net (8.7.1/950822.1) id GAA03533; Thu, 11 Jan 1996 06:59:18 -0500 (EST) Received: by uscmail.usc.es (5.67b/1.34) id AA03510; Thu, 11 Jan 1996 13:00:15 +0100 Date: Thu, 11 Jan 1996 13:00:15 +0100 From: qfsaulo@usc.es (Saulo Vazquez Rodriguez) Message-Id: <199601111200.AA03510@uscmail.usc.es> To: chemistry@ccl.net Subject: classicaltrajectories Dear netters: I would like to acquire a program to calculate microcanonical rate constants and collisional energy transfer rates from classical trajectories. Information about this is appreciated. Thanks in advance. Sincerely, Saulo A. Vazquez (qfsaulo@usc.es) From cscwyt@leonis.nus.sg Thu Jan 11 07:11:58 1996 Received: from sable.nus.sg for cscwyt@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id GAA16321; Thu, 11 Jan 1996 06:53:19 -0500 Received: from leonis.nus.sg (cscwyt@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id TAA31015 for ; Thu, 11 Jan 1996 19:53:14 +0800 Received: (from cscwyt@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id TAA32552; Thu, 11 Jan 1996 19:53:13 +0800 Date: Thu, 11 Jan 1996 19:53:13 +0800 From: Wong Yat-Ting Message-Id: <199601111153.TAA32552@leonis.nus.sg> To: chemistry@www.ccl.net Subject: electrostatic cutoffs in lipid bilayers Cc: cscwyt@leonis.nus.sg Dear Colleagues, I have the following questions. In the past, the electrostatic cutoffs in protein modelling are about 8 to 10 Angstrom. However, in the lipid bilayers, in order to reproduce the experimental results, the cutoffs have to be increased to 30 A. Would you refer me to the correct references concerning the simulation of lipid bilayers with long electrostatic cutoff ? Are there any molecular modeling that requires a cutoff greater than 30 Angstrom ? Thanks. Regards, Yat-Ting Wong From toukie@zui.unizh.ch Thu Jan 11 10:02:41 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id JAA18208; Thu, 11 Jan 1996 09:57:55 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA20292; Thu, 11 Jan 96 15:57:33 +0100 X-Nupop-Charset: Swiss Date: Thu, 11 Jan 1996 16:58:13 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <61093.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Seeking molecular RMS programme Dear Colleagues; I have a collection of Sybyl .mol2 files in DOS format (extension .mol) containing structures of molecules in particular alignments, and which I wish to compare in a pairwise fashion in order to obtain RMS values. Does anyone know of a (stand-alone?) programme that runs under DOS or Windows that will calculate RMS values for pairs of molecular structures encoded in the Sybyl ..mol2 file format or other file format that can be generated from .mol using Babel? If not a programme per se, then does anyone know of a source code of a programme that can do this that can be potentially ported to DOS? Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-8028 ZH 7 Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From P.Wilson@surrey.ac.uk Thu Jan 11 10:47:41 1996 Received: from mailb.surrey.ac.uk for P.Wilson@surrey.ac.uk by www.ccl.net (8.6.10/950822.1) id KAA18784; Thu, 11 Jan 1996 10:37:33 -0500 Received: from central.surrey.ac.uk by mailb.surrey.ac.uk with SMTP (PP); Thu, 11 Jan 1996 15:36:18 +0000 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA17159; Thu, 11 Jan 1996 15:36:12 GMT From: Mr Philip J Wilson Message-Id: <9601111536.AA17159@central.surrey.ac.uk> Subject: potassium basis sets To: CHEMISTRY@www.ccl.net Date: Thu, 11 Jan 96 15:36:03 GMT Mailer: Elm [revision: 70.85] Dear Netters, I would like to attempt to perform some ab initio nuclear shielding calculations on some compounds containing a K atom. In the present Gaussian94 software package only the 3-21G (all electron) and Los Alamos ECP basis sets are available. I would like to hear from anybody who is aware of any other K basis sets (all electron or ECP) which have been tested and shown to be reliable. I will post the replies I receive as soon as possible. Many thanks in advance, Philip Wilson. From jmuilu@joyke7.joensuu.fi Thu Jan 11 15:17:45 1996 Received: from joyx.joensuu.fi for jmuilu@joyke7.joensuu.fi by www.ccl.net (8.6.10/950822.1) id PAA22147; Thu, 11 Jan 1996 15:10:50 -0500 Received: by joyx.joensuu.fi (5.57/Ultrix3.0-C) id AA26224; Thu, 11 Jan 96 22:04:27 +0200 Received: by joyke7.joensuu.fi (NX5.67d/NeXT-2.0) id AA01098; Thu, 11 Jan 96 22:10:42 +0200 Date: Thu, 11 Jan 96 22:10:42 +0200 From: jmuilu@joyke7.joensuu.fi (Juha Muilu) Message-Id: <9601112010.AA01098@joyke7.joensuu.fi> Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: CHEMISTRY@www.ccl.net Subject: Gaussian benchmarks Dear People, GaussianXX benchmark results (test 178) are now on web page http://www.chem.joensuu.fi/people/juha_muilu/Misc/benchmarks.html Best Regards, Juha Muilu Department of Chemistry,University of Joensuu,P.O. Box 111 80101 Joensuu,FINLAND/Email:Juha.Muilu@joensuu.fi,Phone:358-73-1513312, Fax:358-73-1513390,http://www.chem.joensuu.fi/people/juha_muilu From alper@moldyn.com Thu Jan 11 19:17:48 1996 Received: from netcomsv.netcom.com for alper@moldyn.com by www.ccl.net (8.6.10/950822.1) id TAA24894; Thu, 11 Jan 1996 19:04:54 -0500 Received: from moldyn.com by netcomsv.netcom.com with UUCP (8.6.12/SMI-4.1) id PAA02859; Thu, 11 Jan 1996 15:44:40 -0800 Received: by bart.moldyn.com (940816.SGI.8.6.9/940406.SGI.AUTO) id SAA12453; Thu, 11 Jan 1996 18:22:11 -0500 From: alper@moldyn.com (Howard Alper) Message-Id: <199601112322.SAA12453@bart.moldyn.com> Subject: CCL:electrostatic cutoffs in lipid bilayers To: CHEMISTRY@www.ccl.net Date: Thu, 11 Jan 1996 18:22:07 -0500 (EST) Cc: alper@netcom.com (Howard Alper) Reply-To: alper@moldyn.com X-Mailer: ELM [version 2.4 PL22] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1235 Hi, Yat-Ting Wong writes > Dear Colleagues, > > I have the following questions. > > In the past, the electrostatic cutoffs in protein modelling are about 8 > to 10 Angstrom. However, in the lipid bilayers, in order to reproduce > the experimental results, the cutoffs have to be increased to 30 A. Would > you refer me to the correct references concerning the simulation of lipid > bilayers with long electrostatic cutoff ? Are there any molecular modeling > that requires a cutoff greater than 30 Angstrom ? > > Thanks. > > > > Regards, > > Yat-Ting Wong > The articles referred to, concerning the use of 30 angstrom cutoffs in simulations of lipid bilayer systems, are as follows: 1) H. E. Alper, D. Bassolino, and T. R. Stouch, J. Chem. Phys. 98 (12), 9798 (1993) 2) H. E. Alper, D. Bassolino, and T. R. Stouch, J. Chem. Phys. 99 (7), 5547 (1993) Anyone interested in reprints of these, or other articles dealing with diffusion of solutes through lipid bilayers, can send me their address information. Howard Alper -- Dr. Howard Alper Moldyn Inc. 1033 Massachusetts Avenue Cambridge, MA 02138 617-354-3124 x19 - helping molecules find happiness for over a 10th of a century. From elewars@alchemy.chem.utoronto.ca Thu Jan 11 22:32:51 1996 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id WAA25431; Thu, 11 Jan 1996 22:30:32 -0500 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.1/8.7.1) id WAA26946 for chemistry@www.ccl.net; Thu, 11 Jan 1996 22:30:31 -0500 (EST) Date: Thu, 11 Jan 1996 22:30:31 -0500 (EST) From: "E. Lewars" Message-Id: <199601120330.WAA26946@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: REPORT ON A FREQ PROBLEM Hello, some interest was expressed in the problem (see below) I submitted to the Net a couple weeks ago. Some people suggested that the trouble lay in the symmetry changing during Spartan's numerical freq calc (C4v --> Cs), or in instability of the wave- function. I tried to test the wavefunc stability, but that calc flopped with a slew of "unable to assign spin for state..." messages. Since G92 gave the same, reasonable freqs with both analytical and numerical methods, I think the "large imaginary" Spartan freqs are represent a (rare) quirk in that program. The pyramidane and several of its derivatives are relative minima, with of sign of oddball freqs. ======================================== 1995 Dec 25 Hello, I have an interesting problem connected with Spartan. I did an opt/freq on the unusual molecule Me Me \ / Me /C\ Me C------ C \ // \ \ / | \ / | \ /-/------\-\ / | C | C(C-Me)4 Tetramethylpyramidane [/__________\] | / \ | / \ C--------C NOTE: pyramidane, C(CH)4, is / \ / \ a relative minimum (no Me Me Me Me imaginary freqs) at the HF/6-31G*, MP2/6-31G* and C4v MP2/6-31++G** levels. (The HF/6-31G* geom was given in the original mailing) The HF/6-31G* opt proceeded normally (E=-347.628 348), but the freqs are absurd: -68748.51 E -68748.51 E -22116.22 A1 -11996.37 B1 (followed by sensible +ve freqs 151.29 B2 151.88 A2 etc.) ZPE = 566.02 kcal/mol Finding this hard to accept, I used the Spartan HF/6-31G* geom as input for a Gaussian 92 HF/6-31G* opt/freq. The Gaussian opt (which needed only one opt cycle) gave the same E as Spartan (-347.628 348 6) but the freqs and ZPE were quite different (the E from the freq job was also -347.628 348): +163.42 E +163.42 E +164.03 A2 +164.64 B1 +182.69 B2 etc ZPE = 120.42 kcal/mol Has anyone any idea why the two programs gave such different results? I presume that the "huge negative" freqs are simply wrong, and the Gaussian freqs are correct; the parent compound C5H4, and other substituted pyramidanes, gave normal freqs. Thanks for any suggestions. Errol Lewars