From tamasgunda@TIGRIS.KLTE.HU Fri Aug 26 03:41:06 1994 Received: from phem3 for tamasgunda@TIGRIS.KLTE.HU by www.ccl.net (8.6.9/930601.1506) id DAA02891; Fri, 26 Aug 1994 03:11:18 -0400 Received: from HUEARN.SZTAKI.HU (MAILER@HUEARN) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HGCM574APS95ROS6@phem3.acs.ohio-state.edu>; Fri, 26 Aug 1994 03:11:10 EDT Received: from HUKLTE51.BITNET (NJE origin MAILER@HUKLTE51) by HUEARN.SZTAKI.HU (LMail V1.1d/1.7f) with BSMTP id 4819; Fri, 26 Aug 1994 09:09:48 -0400 Received: by tigris.klte.hu (MX V3.3 VAX) id 26362; Fri, 26 Aug 1994 09:08:46 +0100 Date: Fri, 26 Aug 1994 09:08:44 +0100 From: "Tamas Gunda, Hungary" Subject: Re: CCL:logP calculation To: chemistry@ccl.net Reply-to: TAMASGUNDA%HUKLTE51.BITNET@phem3.acs.ohio-state.edu Message-id: <0098384A.895368E0.26362@tigris.klte.hu> Content-transfer-encoding: 7BIT Hello Pau, A good commercial PC program for calculating log P is available from CheMicro Ltd Hegedus Gy. u. 6. H-1136 Budapest Hungary phone: (+36-1)-131 3847 fax: (+36-1)-132 9330 best wishes Tamas ***************************************************************************** Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 tamasgunda@huklte51.bitnet H-4010 Debrecen Hungary ***************************************************************************** From ludek@varda.ics.muni.cz Fri Aug 26 04:41:10 1994 Received: from aragorn.ics.muni.cz for ludek@varda.ics.muni.cz by www.ccl.net (8.6.9/930601.1506) id DAA03219; Fri, 26 Aug 1994 03:59:38 -0400 Received: from varda.ics.muni.cz by aragorn.ics.muni.cz with SMTP id AA16173 (5.67a8/IDA-1.4.4 for ); Fri, 26 Aug 1994 09:59:13 +0200 Received: by varda.ics.muni.cz id AA24127 (5.67a/IDA-1.4.4 for chemistry@ccl.net); Fri, 26 Aug 1994 09:59:12 +0200 Message-Id: <199408260759.AA24127@varda.ics.muni.cz> Subject: CCL: SP2 vs POWER Challenge To: chemistry@ccl.net Date: Fri, 26 Aug 1994 09:59:11 +0200 (MET DST) From: Ludek Matyska X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1707 Dear netters, we in the Czech Republic are in the process of purchasing some ``entry level'' supercomputer-like machines and the decision to be made is between the DEC 7000/630, POWER Challenge and IBM SP2 computers. Due to the budget restrictions we are not able to buy intially anything more powerfull than 4 processor machines, but we expect to get more funding in the forthcoming year(s) (but never more for say 15--20 CPU's). These computers (we will buy 2 of them) will be available for the whole academic (universities) community, but computational chemistry will take a substantial part of their computational resources. I am therefore looking for people with experince of any two of the above mentioned machines, preferably with IBM SP2 and POWER Challenge. We know quite a few (sure not all :-) theoretical pros and contras of the underlying architectures, but we are missing the real experience. I would like to ask you to send me any infromation about the practical comparison between these two architectures, esp. with just a few nodes. Our goal is to start with the use of the facilities as soon as possible after the delivery with the specific target for people for whom the ordinary workstations (SGI, IBM) with up to 128MB RAM are not enough. Thank you very much in advance for any information sent (please send the info directly to me not to bother other uninterested people of the CCL). Sincerely yours, Ludek Matyska Department of Information Technology Faculty of Informatics and Institute of Computer Science Masaryk University Buresova 20 602 00 Brno Fax: ++42-5-41212747 Czech Republic Phone: ++42-5-41321237 ext. 384 e-mail: ludek@ics.muni.cz ++42-5-740267 From nauss@ucmod2.che.uc.EDU Fri Aug 26 07:41:09 1994 Received: from ROCK.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.9/930601.1506) id HAA04123; Fri, 26 Aug 1994 07:22:14 -0400 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-8 #4918) id <01HGCUUR10CW8X1Z1N@UCBEH.SAN.UC.EDU>; Fri, 26 Aug 1994 07:20:51 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:chakravo@cs.purdue.edu id AA12307; Fri, 26 Aug 94 07:41:24 -0400 Date: Fri, 26 Aug 1994 07:41:24 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: CCL:What do Molecular Graphics programs and MM programs do. To: chakravo@cs.purdue.edu (Subhas Chakravorty) Cc: CHEMISTRY@ccl.net Message-id: <9408261141.AA12307@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT I am happy to provide you with my opinions on the matter. The vast majority of my experience has been with semi-empirical or classical calculations. I have had very little experience with ab initio and quantum mechanical calculations. Thus my answers will be a biased. >From chemistry-request@ccl.net Thu Aug 25 22:16:36 1994 >From: chakravo@cs.purdue.edu (Subhas Chakravorty) >What would be a minimum requirement for a program to be termed >as one which models a molecule. >1. Just display the molecule on a screen. Not really. This would more appropriately be called molecular graphics, the visualization of a molecular structure. It is more a computer graphics question than anything else. OTOH one can develope a program by which one could use fragments of molecules to build a complete structure on the screen. In a sense, this type of program would be called a molecular modeling program albeit a very primitive one. >2. Optimise the geometry based on what kind of input ? The input comes from three sources: (1) the cartesian coordinates of the atoms making up the molecues, (2) the internal coordinates of the molecule, i.e. bond lengths, bond angles, torsion angles, (3) other constraints as selected by the user. As a ubiqitous example of the third set of input data, any molecular modelling program will have a set of standard or ideal internal coordinates. The program would then optimize the geometry to minimize deviations from these ideal internal coordinates. The exact means by which this optimization takes place is what differentiates the different force fields and molecular modeling programs. Please note two things. The program could start with either the cartesian coordinates or the internal coordinates. The two are interchangable as soon as you define the coordinates of the first three atoms. Also, the molecular modeling and optimization do not have to involve molecular graphics. It can be and has been done independent of any screen display. >3. What kind of interactions are treated. Name anything. It has probably been studied. Usually the interactions are broken into two major categories: bonded and non-bonded interactions. Bonded interactions are those between any two atoms within three bond lengths of each other. At a minimum they would include bond length, bond angle, and torsion angle energies. (Some folks may argue with me that torsion angle energies are bonded interactions.) Some researchers such as AT Hagler at Biosym Technologies believe strongly in the importance of cross-terms. So they include bond length-bond angle interactions and such. Non-bonded interactions involve London dispersion forces and repulsion terms. One example of these types of interactions is the calculation of non-bonded interactions via the van der Waals equation. Another very important non-bonded interaction is electrostatics, the application of Coulomb's law to the partial charges on the individual atoms. Hydrogen bonding interactions are sometimes explicitly included (e.g. Peter Kollman's AMBER). Finally, the user can define some energy term for some special purpose. These are usually a harmonic function involving distances with the molecule. >4. Do some kind of spectral analysis. I don't see this as part of a molecular modeling program. Rather I see it as a result of data analysis from molecular modeling. If you would please, I would appreciate receiving a summary of your responses. Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC * **************************************************************************** From gregory@wucmd.wustl.edu Fri Aug 26 10:25:44 1994 Received: from wugate.wustl.edu for gregory@wucmd.wustl.edu by www.ccl.net (8.6.9/930601.1506) id KAA07488; Fri, 26 Aug 1994 10:25:44 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA02279; Fri, 26 Aug 1994 09:25:40 -0500 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@ccl.net id AA29942; Fri, 26 Aug 94 08:55:00 -0500 Date: Fri, 26 Aug 1994 08:39:51 -0500 (CDT) From: Gregory Nikiforovich Subject: What molecular modeling means To: chakravo@cs.purdue.edu Cc: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII As any model, the model of a molecule you want to construct, is an image of a real molecule. You cannot build a model, which would account fot ALL properties of your molecule. Therefore, in any case, you will have to choose, which properties of the molecule you need most in THIS PARTICULAR CASE. If you need just to look at the connectivities, molecular graphics (or just image on the screen) would be fine. If you need to solve any conformational problems based on intramolecular energy values, you need to include intra- molecular interactions in your model at the level of atom-atom interactions. If you need to tackle any problem of covalent bond broking, you cannot escape quantum chemistry. And so on. The basic conclusion is, then, as follows: your model (and your software) should be chosen according to your problem, but not vice versa. The first approach is science; the second one is like looking for a lost item just under a street light, but not in the dark street, where it was lost. Well, sometimes it was lost in the right place... Gregory Nikiforovich Research Professor, CMD, WU at St. Louis. From UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca Fri Aug 26 10:41:53 1994 Received: from BANEE.rmc.ca for UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca by www.ccl.net (8.6.9/930601.1506) id JAA06776; Fri, 26 Aug 1994 09:54:55 -0400 From: Message-Id: <199408261354.JAA06776@www.ccl.net> Received: by BANEE.rmc.ca with VINES ; Fri, 26 Aug 94 09:59:43 EDT Date: Fri, 26 Aug 94 08:56:38 EDT Subject: Gaussian SCF packages To: chemistry@ccl.net Does anyone know of any public domain SCF packages that will do ab initio calculations and run on a PC?. How about packages that would take the results of such a program and calculate vibrational spectra and force constants? I would greatly appreciate any help. Thanks Ross Underhill From pballester@cubist.com Fri Aug 26 10:42:33 1994 Received: from nic.near.net for pballester@cubist.com by www.ccl.net (8.6.9/930601.1506) id JAA06813; Fri, 26 Aug 1994 09:56:45 -0400 Received: from cezanne.cubist.com by nic.near.net id aa03685; 26 Aug 94 9:56 EDT Received: from cliff.cubist.com by cezanne.cubist.com (5.0/SMI-SVR4) id AA00764; Fri, 26 Aug 94 09:52:00 EDT Received: from cc:Mail by cliff.cubist.com id AA777919667 Fri, 26 Aug 94 09:47:47 EST Date: Fri, 26 Aug 94 09:47:47 EST From: pballester Message-Id: <9407267779.AA777919667@cliff.cubist.com> To: CHEMISTRY@ccl.net Subject: logP summary content-length: 9829 Hello, Thanks to everybody who responded to my question regarding logP calculation software. Here i is a summary of replies I got to my question. ****************************ANSWERS****************************************** From riusal@redvax1.dgsca.unam.mx Thu Aug 25 22:51:09 1994 I have used Hyperchem and chemplus to do LogP calculation of organic compounds and the agreement is quite good. Chemplus is a program that runs under Hyperchem Autodesk use to market Hyperchem but now is market directly from Hypercube from Canada. With my best regars Carlos ============================================================ From dec@proteus.co.uk Fri Aug 26 07:39:56 1994 Dear Pau I'm not sure if there is a corresponding program available but there was recently a good article on the subject : @article{Klop94 , author = "Klopman, G., Li, J.-Y., Wang, S. and Dimayuga, M. ", title = "Computer Automated log P Calculations Based on an Extended Group Contr ibution Approach ", journal = "Journal of Chemical Information and Computer Sciences ", year = "1994 ", volume = "34 ", pages = "752--781 ", } Best wishes David E. Clark ============================================================= Hello Pau, A good commercial PC program for calculating log P is available from CheMicro Ltd Hegedus Gy. u. 6. H-1136 Budapest Hungary phone: (+36-1)-131 3847 fax: (+36-1)-132 9330 best wishes Tamas ***************************************************************************** Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 tamasgunda@huklte51.bitnet H-4010 Debrecen Hungary ***************************************************************************** ============================================================= From HODGKINE@prince.mm.wyeth.com Fri Aug 26 03:14:48 1994 From: Hodgkin, Ed Date: Fri, Aug 26, 1994 8:43 AM Subject: LogP To: pau@cubist.com Pau I'm also interested in logP calculation. Can you post a summary of replies to the CCL please? Edward Hodgkin Wyeth Research (UK) Ltd hodgkine@prince.mm.wyeth.com ============================================================= Hello Pau, A good commercial PC program for calculating log P is available from CheMicro Ltd Hegedus Gy. u. 6. H-1136 Budapest Hungary phone: (+36-1)-131 3847 fax: (+36-1)-132 9330 best wishes Tamas ***************************************************************************** Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 tamasgunda@huklte51.bitnet H-4010 Debrecen Hungary ***************************************************************************** ============================================================= Dear Dr. Ballester; CompuDrug Chemistry, Ltd. markets a pretty good Windows-based programme called "PrologP 5.0" which enables you to estimate log P values for organic molecules from input structural information. For more information, contact: Dr. Zoltan Bencz, Marketing Director CompuDrug Chemistry, Ltd. Fuerst Sandor utca 5 H-1136 Budapest, Hungary Internet: bz@cdk-cgx.hu or mktg@cdk-cgx.hu FAX-nr: (0036 1) 132-2574 Dr. Bencz is most helpful and fluent in English. Needless to say, PrologP 5.0 is also in English. The programme is relatively simple and straightfor- ward, doesn't require VAX or other expensive, high-power computers/work sta- tions, and you can learn how to use it rather quickly without the assistance of a couple of Ph.D. computational chemists standing behind you. What more can you ask for? Best regards, (Dr.) S. Shapiro Institute fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: (0041 1) 261'56'83 ============================================================= Try CHEMICALC-2 from QCPE. Available in PC and VAX (?) versions Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 ============================================================= From riusal@redvax1.dgsca.unam.mx Thu Aug 25 22:51:09 1994 I have used Hyperchem and chemplus to do LogP calculation of organic compounds and the agreement is quite good. Chemplus is a program that runs under Hyperchem Autodesk use to market Hyperchem but now is market directly from Hypercube from Canada. With my best regars Carlos ============================================================= > Does anybody know of some program or utility to calculate logP > values for organic compounds. Please E-mail directly to me. > I sell a program called MOLGEN which calculates log(p), also, distribution on surface or in a plane of the molecule. The latter calculation is displayable/plottable as a color gradient depiction. It can also calculate conformationally/temperature dependency with respect to log(p). Henry's constant is being added shortly. The program is also a full-featured 3-D modelling program and database with MM2, etc. There is a demo on ccl.net in /pub/chemistry/software/MS-DOS/MOLGEN-demo. Please let me know if I can be of further assistance. PS: I have also used LOGKOW from Syracuse Research, an excellent program, but lacks the feature set in Molgen. Eric _____________________________________________________________________ J. Eric Slone Scientific Consulting Services Serving Government & Industry Since 1982 Internet: eslone@mason1.gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Voice: (703) 461-7078 Miguel do Unamuno ______________________________________________________________________ ============================================================= From shaomeng@helix.nih.gov Thu Aug 25 16:37:32 1994 Dear Pau, We have developed a logP calculation model and the paper concering it has been published in Journal of Chemical Information and Computer Sciences, 1994, Vol. 34, pages 752. I will be gald to send you a reprint if you need. If you are also interested in the program, you can get in touch with Dr. Mario Dimayuga at Case Western Reserve Univ (216)368-3699. I am sure he will be happy to anwser your questions. Hope this will help. With my best regards, -- Ju-Yun Li --- Department of Chemistry Case Western Reserve University Cleveland, Ohio 44106 =========================================================== Computational Chemistry Scientists: I have seen a number of queries on this forum about hydrophobicity. A new program to evaluate HYDROPHOBICITY at the atomistic level recently became available, called HINT. Thanks to Tudor-Ionel Oprea for support comments of HINT. This program is based on empirical data and hydrophobic fragment work of Hansch, Leo, Abraham, and Kellogg. The program can: calculate log P (of small molecules and proteins), score ligand/macromolecule and macromolecule/macromolecule interactions, calculate 3D HYDROPATHY (hydrophobic + hydrophilic) fields, create hydropathic complementarity maps, produce unique 3D hydropathic interaction maps, and is interfaced with InsightII, Sybyl and ChemX. If you are interested in additional information or a free trial of this software, please see the file HINT.note on the CCL archivess (infomeister) or contact me at the address below. You can find a comprehensive list of HINT functionality, the references to publications which describe HINT use, and ordering information in CCL archives. To get it via mail, send a message: select chemistry get info/software-packages/HINT.note to MAILSERV@ccl.net. This file is also available via gopher/anon.ftp/WWW from the /pub/chemistry/info/software-packages/HINT.note on www.ccl.net: gopher www.ccl.net 73 (info/software-packages/Hint.note) -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** ============================================================ A public domain program for calculating logP of small molecules is CHEMICALC-2, available from QCPE for VAX or PC (QCPE 608 or QCMP 129, respectively). Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 ============================================================== Thanks again, Pau Pablo Ballester Cubist Pharmaceuticals, Inc. 24 Emily St. Cambridge MA 02139 E-mail: pau@cubist.com