From owner-chemistry@ccl.net Tue Jul 11 00:53:09 1995 Received: from enar.organik.uni-erlangen.de for jens@EROS.CCC.Uni-Erlangen.DE by www.ccl.net (8.6.10/930601.1506) id AAA00918; Tue, 11 Jul 1995 00:51:04 -0400 Received: from kochab.erosnet (kochab.organik.uni-erlangen.de) by enar.organik.uni-erlangen.de with SMTP id AA08265 for CHEMISTRY@ccl.net (5.65c/IDA-1.4.4/bs-02); Tue, 11 Jul 1995 06:45:44 +0200 Received: by kochab.erosnet (5.x/SMI-4.1/client) id AA02727; Tue, 11 Jul 1995 06:45:42 +0200 Date: Tue, 11 Jul 1995 06:45:42 +0200 From: Jens.Sadowski@EROS.CCC.Uni-Erlangen.DE Message-Id: <9507110445.AA02727@kochab.erosnet> To: CHEMISTRY@ccl.net Subject: Announcement: CORINA as a 2D-to-3D Mail Server Cc: jens@EROS.CCC.Uni-Erlangen.DE X-Sun-Charset: US-ASCII Announcement: CORINA as a 2D-to-3D Mail Server --------------------------------------------------------- 1000 free 3D-structures for everybody! We offer free access to our 2D-to-3D conversion program CORINA via email. This program was recently used to convert the open part of the NCI structural database (~130,000 molecules) which we made public domain. Just mail your 2D-structures and CORINA returns the 3D-atomic coordinates. Send your structure file (MDL MOLFILE format recommended) to corina@EROS.CCC.Uni-Erlangen.de with a subject line reading Props=A_XYZ ReturnFormat=xxx where xxx is the desired return format (the input format is recognized automatically). Return formats are "mol" - MDL MOLFILE, "xyz" - XYZ format, "pdb" - PDB format, "smd" - Standard Molecular Data, "jcamp" - a spectrosopy standard, "compass", "ctx", "molgen", "sharc", "cascii", and "cbin". The mail body is your structure file without any annotations. Possible input formats are all of the above plus SMILES strings and "441". More information at http://schiele.organik.uni-erlangen.de/services/3d.html. ------------------------------------------------------------------------------ | Dr. Jens Sadowski | | | | Computer-Chemie-Centrum Tel.: +49 (0)9131 85-6569 | | Universitaet Erlangen-Nuernberg FAX: +49 (0)9131 85-6566 | | Naegelsbachstrasse 25 Email: Sadowski@EROS.CCC.Uni-Erlangen.DE | | D-91052 Erlangen, Germany | ------------------------------------------------------------------------------ From owner-chemistry@ccl.net Tue Jul 11 03:23:12 1995 Received: from faui45.informatik.uni-erlangen.de for hommes@derioc1.organik.uni-erlangen.de by www.ccl.net (8.6.10/930601.1506) id DAA02492; Tue, 11 Jul 1995 03:11:06 -0400 Received: from derioc1.organik.uni-erlangen.de by uni-erlangen.de with SMTP; id AA22951 (5.65c-7/7.3w-FAU); Tue, 11 Jul 1995 09:07:19 +0200 Received: from q650.organik.uni-erlangen.de by organik.uni-erlangen.de with SMTP; id AA29176 (5.64/7.4b-FAU); Tue, 11 Jul 95 09:07:16 +0200 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 11 Jul 1995 09:07:18 +0200 To: bennett@ubaclu.unibas.ch (Frederick Bennett) From: hommes@derioc1.organik.uni-erlangen.de (Nico van Eikema Hommes) Subject: Re: CCL:g94 on convex Cc: chemistry@ccl.net Hi Fred! > I have tried once or twice to compile g94 on our Convex using the >standard procedure. The helper programs for pre-processing the source are >compiled without problems, but when the time comes to call them during the >make I get this ... >gau-unlimit: Command not found. >gau-arflags: Command not found. > I guess that the makefile needs a bit of doctoring but what I don't know >about Unix scripting could fill an encyclopedia. Has anyone encounterd this >problem and solved it? No modifications to the makefile are necessary, but the environment has to be set up correctly for the installation script to work. Let's assume that you have all the source files in /usr/local/g94. You go into this directory and type (the % is the Unix prompt): % setenv g94root /usr/local i.e. the parent of the g94 directory. Then you run the setup script by typing % source bsd/g94.login which includes necessary directories in your $path. Then, you proceed by typing first % bsd/install to correct permissions, change .f to .F and then you start the actual installation with % bsd/bldg94 >& install.log & (This saves the output of the script, in case something goes wrong). It worked this way on our C220. Good luck! Nico van Eikema Hommes -- Dr. N.J.R. van Eikema Hommes Computer-Chemie-Centrum hommes@ccc.uni-erlangen.de Universitaet Erlangen-Nuernberg Phone: +49-(0)9131-856532 Naegelsbachstr. 25 FAX: +49-(0)9131-856566 D-91052 Erlangen, Germany From owner-chemistry@ccl.net Tue Jul 11 04:08:12 1995 Received: from zrt2.gfz-potsdam.de for mgott@gfz-potsdam.de by www.ccl.net (8.6.10/930601.1506) id DAA02856; Tue, 11 Jul 1995 03:58:03 -0400 Received: by zrt2.gfz-potsdam.de (5.65c/1.34) id AA16164; Tue, 11 Jul 1995 09:57:09 +0200 Received: from exp7.gfz-potsdam.de(139.17.52.31) by zrt2.gfz-potsdam.de via smap (V1.3) id sma016161; Tue Jul 11 09:57:07 1995 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 11 Jul 1995 10:00:43 +0200 To: chemistry@ccl.net From: mgott@gfz-potsdam.de (Matthias Gottschalk) Subject: Viewer for HP worksation Dear Netters, I am looking for a viewer (shareware or public domain) which accepts gaussian94 ouput fo a HP 715 workstation. Xmol seems not to be available for this platform. Any suggestions? Many thanks in advance Matthias Gottschalk Matthias Gottschalk GeoForschungsZentrum Projektbereich 4.1 Postfach 60 07 51 D-14407 Potsdam tel/fax 0 (331) 288-1418/1402 FR Germany intl. tel/fax +49 (331) 288-1418/1402 From owner-chemistry@ccl.net Tue Jul 11 04:20:24 1995 Received: from pereiii.uji.es for pateta@vents.uji.es by www.ccl.net (8.6.10/930601.1506) id EAA02912; Tue, 11 Jul 1995 04:06:36 -0400 Message-Id: <199507110806.EAA02912@www.ccl.net> Received: from migjorn.uji.es by pereiii.uji.es with SMTP (1.37.109.8/16.2) id AA22077; Tue, 11 Jul 1995 10:09:14 +0200 Received: by llevant.uji.es (1.37.109.15/16.2) id AA263160251; Tue, 11 Jul 1995 10:10:51 +0200 From: Augusto Cesar de Camargo Subject: Scian and Gaussian ... To: CHEMISTRY@ccl.net Date: Tue, 11 Jul 1995 10:10:48 +0200 (METDST) Reply-To: X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 1341 Univerisdad Jaume I, July 11 1995 Hi In Jaume I University, Castellon, Spain, We are runing Mopac93, Gaussian 92/94 and Spartan 3.1. I woulk like to know if would be possible create the same graphics of surfaces and volumes obtained in Spartan using Mopac/Gaussian and SciAn. Anyone outside has written sripts or little programs to convert input/otput of Mopac/Gaussian to SciAn input ?? I will summarize the answers. Thank in advance. Augusto Cesar ----------------------------------------+--------------------------------------- | Augusto Cesar de Camargo Neto - Pateta | Keith Nelson: You can't judge a Universitat Jaume I | ------------- book by its cover ... Departament de Ciencies Experimentales | Grupo de Quimica Quantica | Watts: Yeah, but you can tell how Apartat 224 | ----- much it's gonna cost. 12008 - Castello | Spain | in Some Kind of Wonderfull (1987) |--------------------------------------- Phone: +34 64 34-5741 | Fax: +34 64 34-5654 | John Keating: Carpe diem !!! | ------------ e-mail: pateta@migjorn.uji.es | | in Dead Poets Society (1989) ----------------------------------------+--------------------------------------- From owner-chemistry@ccl.net Tue Jul 11 07:23:15 1995 Received: from sable.nus.sg for cscwyt@leonis.nus.sg by www.ccl.net (8.6.10/930601.1506) id HAA04177; Tue, 11 Jul 1995 07:20:55 -0400 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 TAA31581 for ; Tue, 11 Jul 1995 19:20:50 +0800 Received: (from cscwyt@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id TAA03117; Tue, 11 Jul 1995 19:20:49 +0800 Date: Tue, 11 Jul 1995 19:20:49 +0800 From: Wong Yat-Ting Message-Id: <199507111120.TAA03117@leonis.nus.sg> To: chemistry@ccl.net Subject: Hartree-Fock(SCF) calculations on atoms Cc: cscwyt@leonis.nus.sg Dear Colleagues, I am looking for a program that can perform Hartree-Fock(SCF) calculations from hydrogen to radon, preferrably wtih Slater orbitals. The rare-earth metals are not crucial. I know that kind of programs exist long time ago. I would appreciate it if anyone can "dig" it out for me. Thanks. Regards, Yat-Ting Wong cscwyt@nus.sg From owner-chemistry@ccl.net Tue Jul 11 11:38:18 1995 Received: from timbuk.cray.com for shep@appsdiv.cray.com by www.ccl.net (8.6.10/930601.1506) id LAA08600; Tue, 11 Jul 1995 11:28:10 -0400 Received: from ss1.cray.com (shep@ss1.cray.com [128.162.171.15]) by timbuk.cray.com (8.6.12/CRI-8-1.11) with SMTP id KAA24419 for ; Tue, 11 Jul 1995 10:28:10 -0500 Received: by ss1.cray.com (4.1/CRI-5.14) id AA14271; Tue, 11 Jul 95 10:28:09 CDT Date: Tue, 11 Jul 95 10:28:09 CDT From: shep@appsdiv.cray.com (Shepard Smithline) Message-Id: <9507111528.AA14271@ss1.cray.com> To: chemistry@ccl.net Subject: free energies Dear Fellow Computatinal Chemists: Does anyone know of any references that describe the calculation of the anharmonic comtribution to the free energy? One way of doing this would be to implement a free energy perturbation scheme using a harmonic reference system. Does anyone know of someone who has done this? If there is sufficient interest, I will post to the net. Thanks, in advance, Shep Smithline From owner-chemistry@ccl.net Tue Jul 11 12:23:20 1995 Received: from uscmail.usc.es for qfsaulo@usc.es by www.ccl.net (8.6.10/930601.1506) id MAA09702; Tue, 11 Jul 1995 12:20:49 -0400 Received: by uscmail.usc.es (5.67b/1.34) id AA19208; Tue, 11 Jul 1995 18:25:25 +0200 Date: Tue, 11 Jul 1995 18:25:25 +0200 From: qfsaulo@usc.es (Saulo Vazquez Rodriguez) Message-Id: <199507111625.AA19208@uscmail.usc.es> To: chemistry@ccl.net Subject: SGI hardware question Dear netters: We are going to buy a computer to run GAUSSIAN94. We will probably choose one of the two following options from Silicon Graphics: (1) A two-processor (R8000's) PowerChallenge workstation with 128MB RAM (in total) and 6 GB hard disk. (2) Two single-processor PowerChallenge workstations, with 128MB RAM and 4GB hard disk each. Does anybody known which of the two options has a better performance for GAUSSIAN calculations?. Thanks in advance. Saulo A. Vazquez (qfsaulo@usc.es) From owner-chemistry@ccl.net Tue Jul 11 13:23:21 1995 Received: from mail.barrnet.net for brianh@ccl.net by www.ccl.net (8.6.10/930601.1506) id NAA10967; Tue, 11 Jul 1995 13:19:16 -0400 Received: from fujitsu1.fujitsu.com (fujitsu1.fujitsu.com [133.164.254.1]) by mail.barrnet.net (8.6.10/MAIL-RELAY-LEN) with SMTP id KAA06701 for ; Tue, 11 Jul 1995 10:19:15 -0700 Received: from scg.scg.fai.com (scg.scg.fujitsu.com) by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA12086; Tue, 11 Jul 95 10:20:23 PDT Received: by scg.scg.fai.com (4.1/SMI-4.1) id AA00674; Tue, 11 Jul 95 10:19:36 PDT Date: Tue, 11 Jul 95 10:19:36 PDT From: brianh@scg.scg.fujitsu.com (Brian Hammond) Message-Id: <9507111719.AA00674@scg.scg.fai.com> To: chemistry@ccl.net Subject: Call For Papers SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS Monte Carlo Methods in Chemistry 211'th American Chemical Society National Meeting New Orleans March 24-29, 1996 Purpose: This symposium will focus on the use of Monte Carlo in all of computational chemistry. There will be sessions on Monte Carlo in classical dynamics, statistical mechanics, and quantum mechnics, both in theory and applications. Sponsor: The Computers in Chemistry Division of the American Chemical Society. I would like to invite you and your colleagues to participate. This should be a wide ranging session, and there is plenty of room for talks. Please send me an email to indicate interest as soon as possible so I can decide how many sessions to schedule. -Brian ======================================================================== Brian L. Hammond _/_/_/_/ _/_/_/ _/_/_/_/_/ Computational Research Div. _/ _/ _/ _/ Fujitsu America, Inc. _/_/_/ _/_/_/_/_/ _/ 3055 Orchard Drive _/ _/ _/ _/ San Jose, CA 95134 _/ _/ _/ _/_/_/_/_/ Tel: (408) 456-7322 Email: brianh@fai.com From owner-chemistry@ccl.net Tue Jul 11 17:08:35 1995 Received: from monet.chemse.gatech.edu for sahmed@monet.chemse.gatech.edu by www.ccl.net (8.6.10/930601.1506) id RAA16648; Tue, 11 Jul 1995 17:01:08 -0400 Message-Id: <199507112101.RAA16648@www.ccl.net> Received: by monet.chemse.gatech.edu (1.38.193.4/16.2) id AA13877; Tue, 11 Jul 1995 16:55:52 -0400 Date: Tue, 11 Jul 1995 16:55:52 -0400 From: Savant Ahmed To: chemistry@ccl.net Subject: Semi-emperical frequencies Hi, Are there any scaling factors to be used with normal mode frequencies determined from semi-emperical calculations like AM1 and PM3 for hydrocarbons. Thank you. Savant From owner-chemistry@ccl.net Tue Jul 11 18:38:24 1995 Received: from silver.chem.nwu.edu for adrian@silver.chem.nwu.edu by www.ccl.net (8.6.10/930601.1506) id SAA18146; Tue, 11 Jul 1995 18:30:53 -0400 Received: by silver.chem.nwu.edu (950221.405.SGI.8.6.10/921111.SGI.jml) for chemistry@ccl.net id RAA14764; Tue, 11 Jul 1995 17:30:53 -0500 From: adrian@silver.chem.nwu.edu (Adrian Roitberg) Message-Id: <199507112230.RAA14764@silver.chem.nwu.edu> Subject: low T heat capacity To: chemistry@ccl.net Date: Tue, 11 Jul 95 17:30:52 CDT X-Mailer: ELM [version 2.3 PL9] Dear CClers, Do any of you have any pointers to experimental data for specific heat of proteins at VERY low T ? I am specifically interested in BPTI data. Thanks a lot. Adrian E. Roitberg ============================================================================= Dept. of Chemistry | Phone: (708) 491-3423 Northwestern University | Fax : (708) 491-7713 2145 Sheridan Road. Evanston, IL |E-mail:adrian@chem.nwu.edu 60208-3113 | ============================================================================= From owner-chemistry@ccl.net Tue Jul 11 19:08:25 1995 Received: from spider.chemie.fu-berlin.de for sschulz@chemie.fu-berlin.de by www.ccl.net (8.6.10/930601.1506) id TAA18412; Tue, 11 Jul 1995 19:04:32 -0400 Message-Id: <199507112304.TAA18412@www.ccl.net> Received: by spider.chemie.fu-berlin.de (1.37.109.16/16.2) id AA103693870; Wed, 12 Jul 1995 01:04:30 +0200 From: Stefan Schulz Subject: GAMESS graphics programs To: chemistry@ccl.net Date: Wed, 12 Jul 95 1:04:29 MESZ Mailer: Elm [revision: 70.85] Hi, I am looking for a plotting program which can easily be used in conjunction with the ab initio quantum chemistry code GAMESS (US version) and is able to represent molecular orbitals by drawing wiremesh isosurfaces instead of the two-dimensional molecular orbital contour maps produced by PLTORB. A nice user interface and publication quality output would not be bad either. The program should run on HP or SGI Workstations or LINUX PC's. I first tried out Barchetta, but soon noticed that the feature I was looking for was not yet implemented in version 0.2. Any help or comment will be greatly appreciated Stefan Schulz =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Stefan Schulz sschulz@chemie.fu-berlin.de FU Berlin - Theoretical Chemistry Takustrasse 3 D-14195 Berlin =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From owner-chemistry@ccl.net Tue Jul 11 20:38:29 1995 Received: from ailab.ia.ac.cn for zhy@ailab.ia.ac.cn by www.ccl.net (8.6.10/930601.1506) id UAA19108; Tue, 11 Jul 1995 20:33:11 -0400 Received: by ailab.ia.ac.cn id AA00369 (5.67b/IDA-1.5 for chemistry@ccl.net); Wed, 12 Jul 1995 09:34:31 +0900 Date: Wed, 12 Jul 1995 09:34:31 +0900 From: Zhang HongYu Message-Id: <199507120034.AA00369@ailab.ia.ac.cn> To: chemistry@ccl.net Subject: summary of "grid representation of protein potential" Hi, Thanks to all the replies concerning my question of "Grid representation of protein potential". >Is there any code available which represents the force field >(such as ECEPP,CHARMm) or molecular volume of a protein by a grid? Here is a summary and welcome more infomation if any. ---------------------------------------------------------------------------------- From: Nathaniel (noj) Malcolm I reccomend that you have a look at the work of A. Warshel, he has been using Langevin Dipoles on a grid to represent proteins and solvents for some time. Noj Noj.Malcolm@man.ac.uk From: Mr Andrew D Allen Dear Henry Hongyu Zhang, Try contacting :- wasserzr@lldmpc.dnet.dupont.com, hodgecn@lldmpc.dnet.dupont.com (Nick Hodge), thacher@biosym.com (Tom Thacher) They are working on BForce, which should go into the Biosym software suite, (hopefully for the next release). The preliminary information seems to fit what you are looking for. Andy -- ############################################################################## Structural and Computation Chemistry Group________chp1aa@uk.ac.surrey - JANET. Department of Chemistry___________________________phone_______+44-1483-259591. University of Surrey______________________________fax_________+44-1483-259514 Guildford,________________________________________ftp___________131.227.110.69 Surrey, GU2 5XH, UK_________________WWW http://www.chem.surrey.ac.uk/~chp1aa/ ############################################################################## From: stoutepf@chemsci5.dmpc.com (Pieter Stouten) Dear HongYu, At 11:21 95/07/02, you wrote: >Is there any code available which represents the force field >(such as ECEPP,CHARMm) or molecular volume of a protein by a grid? > I am not sure exactly what you are looking for. I assume you want to do EM or MD with a grid representation of (the bulk of) a protein. We have developed a method that is currently implemented in Amber and Biosym's Discover. Relevant papers are: * P.F.W. Stouten, C. Frvmmel, H. Nakamura & C. Sander, "An Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations," Mol. Simulation 10 (1993) 97-120. * B.A. Luty, Z.R. Wasserman, P.F.W. Stouten, C.N. Hodge, M. Zacharias & J.A. McCammon, "A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions," J. Comp. Chem. 16 (1995) 454-464. Please let me know if you would like to receive reprints. Cheers, Pieter. -- Pieter Stouten, Senior Research Scientist || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80353, Wilmington, DE 19880-0353 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Internet: stoutepf@chemsci5.dmpc.com || Indiana Jones From: wujih Hello, Mr. zhang, it is nice to see the email from china. As for your question, what do you actually means when you say 'to represent the force field or molecular volume of a protein? is it to map them on a grid? Do you got UHBD4.01 or Python program? Have a try. Cheers, Wu J H PhD in computer modelling Chem. Department Univ. of Essex Colchester CO4 3SQ U.K. email wujih@essex.ac.uk