From chemistry-request@server.ccl.net Wed Mar 22 08:45:57 2000 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA17438 for ; Wed, 22 Mar 2000 08:43:27 -0500 Received: from qogolem (qogolem.usc.es [193.144.74.235]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id OAA17376 for ; Wed, 22 Mar 2000 14:42:59 +0100 (MET) From: "Armando Navarro" To: Subject: d pure functions in GAMESS Date: Wed, 22 Mar 2000 14:34:16 +0100 Message-ID: <01bf9403$51c9b6d0$eb4a90c1@qogolem.usc.es> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Dear All: I have been doing some MP2/6-311+G** calculations with PC-GAMESS, GAMESS used 6 d cartesian functions insted of pure d functions. Is it possible to use the 5 pure d functions in GAMESS? Thanks in Advance Armando Navarro Departamento de quimica Organica Facultade de qumica Universidade de Santiago de Compostela e-mail qoajnv@usc.es From chemistry-request@server.ccl.net Wed Mar 22 07:35:48 2000 Received: from rs5.thch.uni-bonn.de (rs5.thch.uni-bonn.de [131.220.44.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA17230 for ; Wed, 22 Mar 2000 07:35:47 -0500 Received: (from bernd@localhost) by rs5.thch.uni-bonn.de (8.8.8/8.8.5) id NAA13933 for chemistry@www.ccl.net; Wed, 22 Mar 2000 13:37:27 +0100 From: Bernd Engels Message-Id: <200003221237.NAA13933@rs5.thch.uni-bonn.de> Subject: electrostatic potential To: chemistry@server.ccl.net (Computational Chemistry List) Date: Wed, 22 Mar 100 13:37:26 +0100 (MEZ) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear All, Somebody from here want to plot the electrostatic potential which he computed with G98 (gaussian cube file). Which plot program is the best. Bernd Engels Inst. für Org. Chemie Universität Würzburg From chemistry-request@server.ccl.net Wed Mar 22 07:54:13 2000 Received: from gpo.cam.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA17285 for ; Wed, 22 Mar 2000 07:54:12 -0500 Received: from trafford (dhcp33.cam.msi-eu.com [172.27.65.33]) by gpo.cam.msi-eu.com (8.9.3/8.9.3/Debian/GNU) with SMTP id MAA23393 for ; Wed, 22 Mar 2000 12:51:43 GMT Message-Id: <3.0.32.20000322125142.009eb150@mailhost.msicam.co.uk> X-Sender: stephen_warde@mailhost.msicam.co.uk X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 22 Mar 2000 12:51:43 +0000 To: chemistry@ccl.net From: Steve Warde Subject: Computational Materials Science Seminars Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCL-ers, During May, Molecular Simulations Inc. is organising a series of free scientific seminars in the US and Europe. These will cover topics in computational materials science, including crystallization, catalysis, and polymer modeling. They feature speakers from industry, government laboratories, academia, and MSI. For details see http://www.msi.com/matseries/ I hope that these will be of use to some list subscribers. Best wishes, Steve Warde MSI From chemistry-request@server.ccl.net Wed Mar 22 09:39:28 2000 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA17825 for ; Wed, 22 Mar 2000 09:39:28 -0500 Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with ESMTP id PAA28070 for ; Wed, 22 Mar 2000 15:39:16 +0100 (MET) Received: from pc04.chemie.uni-jena.de by pc04.chemie.uni-jena.de (8.8.8/1.1.22.3/02Dec99-0338PM) id PAA0000004441; Wed, 22 Mar 2000 15:39:15 +0100 (MET) Sender: goeller@pc04.chemie.uni-jena.de Message-ID: <38D8DB12.D44852FE@pc04.chemie.uni-jena.de> Date: Wed, 22 Mar 2000 15:39:14 +0100 From: Andreas Goeller X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: German, de, en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: UV/vis visualisation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, >from semiempirical calculations I get transition energies (say, in wavenumbers, lam) and oscillator strengths (osc), i.e. a line spectrum. The osc are proportional to the surface below one extinction curve. I can model this curve approximately by using a Gauss curve f(x), and by summation over all curves (g(x)) I get something comparable to an experimental spectrum. The function is g(x)= sum_i(osc_i*(fx_i)) f(x)= 1/(sigma*sqrt(2*pi))*exp(-0.5*((x-x0)/sigma)**2) Can anybody give me a hint about reasonable choices for sigma, the standard deviation? The smaller sigma, the steeper the curve. Thanks a lot for the answers I hope to get -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Mar 22 10:09:17 2000 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18073 for ; Wed, 22 Mar 2000 10:09:13 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id RAA10280 for ; Wed, 22 Mar 2000 17:06:57 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Wed, 22 Mar 2000 17:06:57 +0200 (EET) From: Mikael Johansson X-Sender: mpjohans@soul.helsinki.fi To: chemistry@ccl.net Subject: HyperChem .hin-file to PDBQ converter: hin2pdbq.py In-Reply-To: <01bf9403$51c9b6d0$eb4a90c1@qogolem.usc.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! If someone thinks he/she could use a little proggie that converts HyperChem .hin-files to PDBQ-files (for use with for example AutoDock) feel free to download it from: http://www.helsinki.fi/~mpjohans/python/ I wrote it because I couldn't find any converter that would have kept the charges on the atoms. The program is written in Python, so you will need a Python interpeter (everyone should have one :-) If you find anything to comment on, please do. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi From chemistry-request@server.ccl.net Wed Mar 22 10:13:27 2000 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18096 for ; Wed, 22 Mar 2000 10:13:27 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id RAA01960 for ; Wed, 22 Mar 2000 17:11:08 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Wed, 22 Mar 2000 17:11:08 +0200 (EET) From: Mikael Johansson X-Sender: mpjohans@soul.helsinki.fi To: chemistry@ccl.net Subject: AutoDock 3.00/3.0.5 difference? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! I'm just about to start doing something serious with AutoDock. The version we have here is 3.00, but the latest released version is, if I understand correctly, 3.0.5. So what has changed, and would an upgrade be recommended? Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi From chemistry-request@server.ccl.net Wed Mar 22 10:08:26 2000 Received: from mail.science.siu.edu (mail.science.siu.edu [131.230.107.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18067 for ; Wed, 22 Mar 2000 10:08:22 -0500 Received: from tapas (131.230.99.83) by mail.science.siu.edu with SMTP (Eudora Internet Mail Server 2.2.2); Wed, 22 Mar 2000 09:07:19 -0600 Message-ID: <004601bf9410$3dc87c40$5363e683@thchem.siu.edu> From: "Tapas Kar" To: "Bernd Engels" , "Computational Chemistry List" References: <200003221237.NAA13933@rs5.thch.uni-bonn.de> Subject: Re: CCL:electrostatic potential Date: Wed, 22 Mar 2000 09:06:46 -0600 Try Chem3D ---------------------------------------------------- Tapas Kar Department of Chemistry 1245 Lincoln Dr. # 146F Southern Illinois University Carbondale, IL 62901-4409 Tel: 618-453-6485(Off)/6433(Lab) Fax: 618-453-6408 email: tapaskar@siu.edu tapas@risky3.thchem.siu.edu ----- Original Message ----- From: Bernd Engels To: Computational Chemistry List Sent: Wednesday, March 22, 2000 9:05 AM Subject: CCL:electrostatic potential > Dear All, > > Somebody from here want to plot the electrostatic potential which he computed > with G98 (gaussian cube file). > > Which plot program is the best. > > Bernd Engels > Inst. für Org. Chemie > Universität Würzburg From chemistry-request@server.ccl.net Wed Mar 22 10:53:01 2000 Received: from mailhost.rdg.ac.uk (exim@sumh1.rdg.ac.uk [134.225.16.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18365 for ; Wed, 22 Mar 2000 10:53:00 -0500 Received: from indyp.chemistry ([134.225.168.35] helo=reading.ac.uk) by mailhost.rdg.ac.uk with esmtp (University of Reading Email Service) id {12XnR3-0001r9-00} for CHEMISTRY@www.ccl.net; Wed, 22 Mar 2000 15:52:41 +0000 Sender: dave@ccl.net Message-ID: <38D8EBD8.6381D052@reading.ac.uk> Date: Wed, 22 Mar 2000 15:50:48 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.72 [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: MM vdW potential function derivation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am trying to parameterise a system for use in molecular mechanics/molecular dynamics/monte carlo calculations. I have seen little in the literature about this (eg electron gas method, HF/DFT calcs for torsional angles), has anyone published a comprehensive review or have any very useful programs for this sort of thing? I will summarise any answers I get if there is an interest. (Please don't tell me to use the universal force-field). Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Wed Mar 22 12:21:49 2000 Received: from tdsede-exg.tdsede.dom ([194.235.134.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA19259 for ; Wed, 22 Mar 2000 12:21:46 -0500 Received: by TDSEDE.EXG with Internet Mail Service (5.5.2232.9) id ; Wed, 22 Mar 2000 15:33:27 -0000 Message-ID: <314CB0E40556D2118D930000C07CAAF606F820@TDSEDE.EXG> From: Paulo Couto To: CHEMISTRY@ccl.net Cc: Armando Navarro Subject: RE: d pure functions in GAMESS Date: Wed, 22 Mar 2000 15:33:26 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain Greetings All To use Spherical Harmonics, i.e. 5d functions, you need to include ISPHER=1 in the $CONTRL Section. Paulo Couto (pcouto@alf1.cii.fc.ul.pt) > -----Original Message----- > From: Armando Navarro [SMTP:qoajnv@usc.es] > Sent: Wednesday, March 22, 2000 1:34 PM > To: CHEMISTRY@ccl.net > Subject: CCL:d pure functions in GAMESS > > Dear All: > I have been doing some MP2/6-311+G** calculations with PC-GAMESS, > GAMESS used 6 d cartesian functions insted of pure d functions. Is it > possible to use the 5 pure d functions in GAMESS? > > Thanks in Advance > Armando Navarro > Departamento de quimica Organica > Facultade de qumica > Universidade de Santiago de Compostela > > e-mail qoajnv@usc.es > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > From chemistry-request@server.ccl.net Wed Mar 22 13:23:58 2000 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA19816 for ; Wed, 22 Mar 2000 13:23:56 -0500 Received: (qmail 29877 invoked from network); 22 Mar 2000 18:23:22 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 22 Mar 2000 18:23:22 -0000 Received: (qmail 7850 invoked from network); 22 Mar 2000 18:20:24 -0000 Received: from egppp2.physics.upatras.gr (HELO stelios) (150.140.159.94) by pythagoras.physics.upatras.gr with SMTP; 22 Mar 2000 18:20:24 -0000 Message-ID: <028101bf942b$835edcc0$5e9f8c96@stelios> From: "garoufal" To: Subject: G94 and PVM Date: Wed, 22 Mar 2000 20:21:58 +0200 Dear CCL'ers We have just made up and testing a linux cluster of 4 boxes, and I wonder if it is possible to to run g94 in parallel using the PVM. ____________________________________ Christos S. Garoufalis Dept. of Physics, University of Patras, Greece ____________________________________ From chemistry-request@server.ccl.net Wed Mar 22 14:04:06 2000 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA20042 for ; Wed, 22 Mar 2000 14:04:06 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id OAA26316; Wed, 22 Mar 2000 14:03:47 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <38D91A39.5BE1F4E6@syr.edu> Date: Wed, 22 Mar 2000 14:08:41 -0500 From: Deepak Singh Organization: Birge Group, Dept. Of Chemistry, Syracuse Univ. X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Dave Price CC: Comp Chem Mailing List Subject: Re: CCL:MM vdW potential function derivation References: <38D8EBD8.6381D052@reading.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Price, There is a paper by MacKerell et al (J. Phys. Chem B, 102, 3586-3616, 1998) that covers the methods that the authors use to parametrize the CHARMM forcefield. That should be useful to you. GAMESS which is free is probably what you neeed (or Gaussian98) for any parametrization. regards Deepak. Dave Price wrote: > Dear CCLers, > I am trying to parameterise a system for use in molecular > mechanics/molecular dynamics/monte carlo calculations. I have seen > little in the literature about this (eg electron gas method, > HF/DFT calcs for torsional angles), has anyone published a comprehensive > review or have any very useful programs for this sort of thing? > I will summarise any answers I get if there is an interest. > (Please don't tell me to use the universal force-field). > Cheers, > Dave > > -- > ------------------------------------------------------------------------ > > Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 > Department of Chemistry, Fax: +44 (0)118 9316331 > University of Reading, mailto:d.w.price@reading.ac.uk > Whiteknights, > READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html > RG6 6AD > U.K. > > ------------------------------------------------------------------------ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Wed Mar 22 15:59:56 2000 Received: from yakko.cimav.edu.mx (root@[207.248.161.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA20481 for ; Wed, 22 Mar 2000 15:59:54 -0500 Received: from glossman ([207.248.161.148]) by yakko.cimav.edu.mx (8.9.3/8.9.3) with SMTP id OAA27044 for ; Wed, 22 Mar 2000 14:06:01 -0700 Message-ID: <019f01bf9449$2753f3c0$94a1f8cf@cimav.edu.mx> From: "Dr. Daniel Glossman" To: "Computational Chemistry List" Subject: scaling factor Date: Wed, 22 Mar 2000 13:54:05 -0800 Dear netters: Can somebody point me to a reference for the vibrational scaling factor for a B3LYP/6-31G(d,p) frequency calculation? I already know the value (0.9613) for a B3LYP/6-31G(d) from the paper of Wong CPL 256, 391 (1996). Thanks in advance. Best regards Dr. Daniel Glossman Mitnik *************************************************************************= Dr. Daniel Glossman Mitnik Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) Departamento de Pol=EDmeros = Phone: (52) 1 4391151 Miguel de Cervantes 120 = FAX: (52) 1 4391112 Complejo Industrial Chihuahua = E-mail: glossman@mail.cimav.edu.mx Chihuahua, Chih. 31109 = glossman@hotmail.com Mexico *************************************************************************= From chemistry-request@server.ccl.net Wed Mar 22 23:28:10 2000 Received: from si.fi.ameslab.gov (si.fi.ameslab.gov [147.155.20.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA22343 for ; Wed, 22 Mar 2000 23:28:07 -0500 Received: (from pradipta@localhost) by si.fi.ameslab.gov (AIX4.2/UCB 8.7/8.7) id WAA30268 for chemistry@ccl.net; Wed, 22 Mar 2000 22:28:09 -0600 (CST) From: Pradipta Bandyopadhyay Message-Id: <200003230428.WAA30268@si.fi.ameslab.gov> Subject: IPCM! To: chemistry@ccl.net (CCL) Date: Wed, 22 Mar 2000 22:28:09 -0600 (CST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Hi everyone, What is value of the density used in the isodensity surface construction in the IPCM model ( I mean what is the default value in GAUSSIAN 94)? Also the unit of the solute cavity in the IPCM model - is it Angstrom3 (cube)?. Thanks. Pradipta -- ------------------------------------------------------------------------------ You may my glories and my state dispose, But not my griefs; still am I king of those. -- William Shakespeare, "Richard II" ------------------------------------------------------------------------------