From qibvigap@lg.ehu.es Thu Mar 13 04:29:01 1997 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id DAA09292; Thu, 13 Mar 1997 03:29:58 -0500 (EST) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA29766; Thu, 13 Mar 97 09:27:46 GMT Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA18645; Thu, 13 Mar 1997 09:36:40 GMT Date: Thu, 13 Mar 1997 09:36:39 +0000 (WET) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: TZV basis sets of Schafer, Huber and Ahlrichs Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I tried to download the TZV basis sets, as well as other ones, from 129.13.107.186, as indicated in J. CHem. Phys. 1992,97(4),2571 J. Chem. Phys. 1994,100(8),5829. but the FTP server does not accept "anonymous" as login. Does anybody know if these basis sets have been moved to other server, and how I can get them? Thanks a lot for your help Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From peon@medchem.dfh.dk Thu Mar 13 04:35:50 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id EAA09622; Thu, 13 Mar 1997 04:14:00 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id KAA21140; Thu, 13 Mar 1997 10:13:58 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id LAA04557; Thu, 13 Mar 1997 11:41:09 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 13 Mar 1997 10:14:00 +0100 To: ahocquet@tamarugo.cec.uchile.cl From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:the MM2 (big) family Cc: chemistry@www.ccl.net Dear Alexandre, The list of MM2s you gave is a good starting point. I do have a few additions. First, I think you should list all the cases where Allinger himself drastically changed the functional form. The original version is MM2(77), and MMP2 came as a separate program in 1980 (I think, I'm not entirely sure of all dates I'll give below). The MM2(85) combined MM2 and MMP2 into one program, so that is a functional change. With this version, MM2 reached a kind of maturity plateau. There were later changes, but not any drastic improvements in overall performance. There were new versions in 1987 and 1991, and at least the MM2(87) version included changes in functional form. There are many "minor" functions in MM2, like electronegativity effect and anomeric effect, I cannot say for sure when they were added, but I believe that all were in MM2(87). I think MM2(91) was just a parameter update, but I'm not sure. In 1994 was published the parameter estimator for MM2 (and MM3), "J. Mol. Struct (THEOCHEM) 312 (1994) 69-83", but I haven't seen an implementation for MM2 (it is in MM3[94]). Other implementations: TINKER, from Jay Ponder (info at http://dasher.wustl.edu/) The Chem3D parameters were originally from TINKER You lacked a reference for Chem3D, see: http://www.camsci.com/ CAChe from Tektronix has an "augmented" MM2. Spartan from Wavefunction includes an MM2 with the original parameter set, but no conjugated calculations! A bit dangerous, but... See: http://www.wavefun.com/ In the MacroModel manual I also found references to Osawa, "Tet, 2769 (83)", and Kroon-Batenburg, "JMolStr, 417 (83)", I don't know if both qualify as separate implementations according to your rules. I know that several workers in the inorganic/organometallic field have extended MM2 to higher coordination. You could use the review by Benjamin Hay as a starting point, "Coord. Chem. Rev. 126, 177-236 (1993)". Many (I'm among them) have also solved special coordinations in MM2 without changes to the functional form using tricks like dummy atoms and fixed atoms, I don't know if that qualifies ( MM2 definitely wasn't INTENDED to be abused so, that's for sure... :-). Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From pobirbaa@sq.ehu.es Thu Mar 13 05:29:00 1997 Received: from scsx01.sc.ehu.es for pobirbaa@sq.ehu.es by www.ccl.net (8.8.3/950822.1) id EAA09828; Thu, 13 Mar 1997 04:43:55 -0500 (EST) Received: from scdx01.sc.ehu.es (root@scdx01.sc.ehu.es [158.227.150.50]) by scsx01.sc.ehu.es (8.8.4/8.7.3) with SMTP id KAA27476 for ; Thu, 13 Mar 1997 10:45:55 +0100 (MET) Status: N Received: from sqpp99.sq.ehu.es by scdx01.sc.ehu.es (5.65/4.7) id AA12678; Thu, 13 Mar 1997 10:45:52 GMT Message-Id: <9703131045.AA12678@scdx01.sc.ehu.es> X-Sender: pobirbaa@158.227.150.50 X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 1 (Highest) Date: Thu, 13 Mar 1997 10:45:12 -0500 To: chemistry@www.ccl.net From: pobirbaa@sq.ehu.es (Arantxa Irigoras Balda) Subject: diamagnetic... Dear CClers, Does anyone know about any reference for experimental data on 1. Nuclear magnetic shielding constant (diamagnetic shielfing factor) 2. Diamagnetic susceptibility of atoms and molecules? Thanks in advance. Arantxa Irigoras. Ph.D. Student Kimika Fakultatea. E.H.U. P.K. 1072; 20080 DONOSTIA EUSKADI (SPAIN) Fax.:+3443 212236 Telef.:+3443 216600 Ext.:127 e_mail: POBIRBAA@SQ.EHU.ES From aentrena@goliat.ugr.es Thu Mar 13 08:29:03 1997 Received: from goliat.ugr.es for aentrena@goliat.ugr.es by www.ccl.net (8.8.3/950822.1) id HAA10412; Thu, 13 Mar 1997 07:32:11 -0500 (EST) Received: from quimfarm3.ugr.es (quimfarm3.ugr.es [150.214.65.62]) by goliat.ugr.es (8.8.5/8.7.3) with SMTP id NAA25879 for ; Thu, 13 Mar 1997 13:29:43 +0100 (MET) Sender: entrena@goliat.ugr.es Message-ID: <332871CC.2781@goliat.ugr.es> Date: Thu, 13 Mar 1997 13:29:48 -0800 From: Antonio Entrena Guadix X-Mailer: Mozilla 2.01S (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: CCL Subject: Printer for a SGI Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all: I am interesting in printers for a SGI workstation that can be used to print both text and graphics, prefereably in color, and no too expensive. The main use for this printer is to generate graphics of molecules calculated with Sybyl. Can anyone indicate to me some model(s) which give good results? Thanks to all Sinceresly -- ************************************************************************** Dr. Antonio Entrena Guadix Phone: (34)-(9)58-243849 Departamento de Quimica Organica Fax: (34)-(9)58-243845 Facultad de Farmacia E-mail: entrena@quimfarm3.ugr.es Campus de Cartuja s/n aentrena@goliat.ugr.es 18071 GRANADA (SPAIN) ************************************************************************** From alain.kessi@psi.ch Thu Mar 13 08:32:15 1997 Received: from psizi1.psi.ch for alain.kessi@psi.ch by www.ccl.net (8.8.3/950822.1) id HAA10433; Thu, 13 Mar 1997 07:39:08 -0500 (EST) Received: from localhost by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA21192; Thu, 13 Mar 1997 13:34:54 +0100 Sender: kessi@psizi1.psi.ch Message-Id: <3327F468.500F@psi.ch> Date: Thu, 13 Mar 1997 13:34:48 +0100 From: Alain Kessi Organization: Paul Scherrer Institut, Zuerich, Switzerland X-Mailer: Mozilla 3.0 (X11; I; AIX 2) Mime-Version: 1.0 To: Pablo Vitoria Garcia Cc: CCL Computational Chemistry List Subject: Re: CCL:TZV basis sets of Schafer, Huber and Ahlrichs References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Pablo Vitoria Garcia wrote: > I tried to download the TZV basis sets, as well as other ones, from > 129.13.107.186, as indicated in > > J. CHem. Phys. 1992,97(4),2571 > J. Chem. Phys. 1994,100(8),5829. > > but the FTP server does not accept "anonymous" as login. It's never a good idea to indicate hosts by their numbers. A quick look at "nslookup 129.13.107.186" shows me that the host is called "tchibm3.chemie.uni-karlsruhe.de" in "real life", which leads me to try "ftp ftp.chemie.uni-karlsruhe.de", which works (a miracle! :-), and where you can actually find the basis sets. Alain -- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zurich ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ From underhil@me2.rmc.ca Thu Mar 13 09:29:03 1997 Received: from serveri.rmc.ca for underhil@me2.rmc.ca by www.ccl.net (8.8.3/950822.1) id JAA11041; Thu, 13 Mar 1997 09:19:11 -0500 (EST) Message-Id: <199703131419.JAA11041@www.ccl.net> Received: from underhill.rmc.ca by sv2.rmc.ca with SMTP (1.37.109.15/16.2) id AA058842779; Thu, 13 Mar 1997 09:19:39 -0500 Date: Thu, 13 Mar 1997 09:19:39 -0500 X-Sender: underhil@137.94.5.141 X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: underhil@me2.rmc.ca (Ross Underhill) Subject: Parameters for Silanes I'm looking for molecular mechanics parameters for silanes, especially torsional parameters such as H-O-SI-O and H-O-SI-C4. I'm not too concerned about which forcefield at the moment. I would appreciate it if people could pass on any references they are aware of. ALso, if there's anyone out there working on these I'ld love to know who you are. Thanks in advance Dr. Ross Underhill Royal Military College of Canada Kingston, Ontario K7K 5L0 (613) 541-6000 X6175 From ccl@www.ccl.net Mon Mar 10 21:36:26 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id VAA18811; Mon, 10 Mar 1997 21:20:41 -0500 (EST) Received: from entropy.ucsc.edu for richmc@entropy.ucsc.edu by bedrock.ccl.net (8.8.3/950822.1) id VAA22928; Mon, 10 Mar 1997 21:20:40 -0500 (EST) Received: (qmail 24633 invoked by uid 500); 11 Mar 1997 02:20:41 -0000 From: "Rich McClellan" Message-Id: <9703101820.ZM24631@entropy.ucsc.edu> Date: Mon, 10 Mar 1997 18:20:40 -0800 X-Mailer: Z-Mail (3.2.1 24feb96 Caldera) To: chemistry@ccl.net Subject: Re: CCL: G94 on LINUX Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > Dear Members of CCL: > Last week I posed a question about problems compiling G94.D4 on > RedHat Linux 4.0. I have had a number of interesting replies which > I plan to summarize. But I still have a problem. > Gaussian, Inc. wrote me to suggest a hardware problem. It turns > out this this is quite likely the actual problem. But how to fix? > It seems that I have a faulty memory chip. My computer, a Gateway > P6 has 64 Mbytes of new memory. The machine says all is ok on boot- > up. But I have random problems with the C-compiler quitting. > So maybe there is a memory problem. Gaussian suggested removing > or switching memory. Now it appear I can compile the program > with only 2x16 Mbytes of memory. > So the question is, how does one test memory? OK, the computer > thinks the memory is ok. But all the boot-up test is doing is > writing 1, 0 into memory and then seeing if it is still there > in a few microseconds. But it would seem that to compile and run > a big FORTRAN program, one would be interested in having this > same test performed 10 seconds later. How then does one test the > long-term refresh function of big memory blocks? > Regards, Dave Close. There are two ways of testing your memory without rebooting your Linux box to another OS. The first is to use memtest available from a mirror near you (or entropy.ucsc.edu/pub/linux/memtest86-1.1.tar.gz). The second is a series of kernel makes. You can read more about the second at http://www.bitwizard.nl/sig11/ good luck, Rich From cresimm@POP.univ-lille1.fr Wed Mar 12 09:28:49 1997 Received: from lilserv.univ-lille1.fr for cresimm@POP.univ-lille1.fr by www.ccl.net (8.8.3/950822.1) id IAA02586; Wed, 12 Mar 1997 08:56:22 -0500 (EST) Received: from omega.univ-lille1.fr (omega.univ-lille1.fr [134.206.1.35]) by lilserv.univ-lille1.fr (8.7.6/jtpda-5.1) with SMTP id PAA10293 for ; Wed, 12 Mar 1997 15:00:37 +0100 (MET) Received: by omega.univ-lille1.fr; id AA09046; Wed, 12 Mar 1997 14:56:18 +0100 Message-Id: <9703121356.AA09046@omega.univ-lille1.fr> X-Sender: cresimm@pop.univ-lille1.fr X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 12 Mar 1997 16:01:16 -0100 To: chemistry@www.ccl.net From: CRESIMM Subject: CCL: porphyrins Dear netters I am just in the beginning of preparation of my thesis. I would greatly appreciate receiving an information(references of recent reviews ,etc...)about the present state of the art in the field of molecular mechanics/quantum chemical calculations and vibrational spectroscopy(Raman,Resonnance raman)of porphyrins and porphyrins containing proteins. Any advise is greatly appreciated. Thank you TAZI MOUHSINE From gomide@power.ufscar.br Wed Mar 12 17:28:55 1997 Received: from power.ufscar.br for gomide@power.ufscar.br by www.ccl.net (8.8.3/950822.1) id RAA06323; Wed, 12 Mar 1997 17:24:58 -0500 (EST) Received: by power.ufscar.br (940816.SGI.8.6.9/911001.SGI) id TAA03041; Wed, 12 Mar 1997 19:21:12 -0300 Date: Wed, 12 Mar 1997 19:21:10 -0300 (BST) From: "Luiz C. Gomide" To: LONGO@NPD.UFPE.BR cc: chemistry@www.ccl.net Subject: Re: CCL:Solvent mutation In-Reply-To: <01IGE5TWAJ828X1ISQ@NPD.UFPE.BR> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Longo, the best thing to do is: - solute mutation to a dummy in water - solute mutation to a dummy in methanol You will get the free energy of transfer. By L C Gomide Freitas DQ-UFSCAR-BRAZIL On Tue, 11 Mar 1997 LONGO@NPD.UFPE.BR wrote: > > Hi there, > > Could anyone give me some pointers or references of MC or MD > simulations involving **solvent** mutation? That is, the solute > is kept the same during simulation, but the solvent is changed > eg., water to methanol, so that you can get the free energy > difference of going from one solvent to the other? > > Thanks a lot, > > Ricardo Longo > longo@npd.ufpe.br > DQF-UFPE - Brazil > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: LONGO@NPD.UFPE.BR > -- Original Sender From: Address: LONGO@NPD.UFPE.BR > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From SMILLER@RARUSRAEXS1.prius.jnj.com Thu Mar 13 11:32:25 1997 Received: from smtp-internet.jnj.com for SMILLER@RARUSRAEXS1.prius.jnj.com by www.ccl.net (8.8.3/950822.1) id KAA11772; Thu, 13 Mar 1997 10:41:24 -0500 (EST) Received: by smtp-internet.jnj.com id AA05026 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Thu, 13 Mar 1997 10:40:34 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-2); Thu, 13 Mar 1997 10:40:34 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-1); Thu, 13 Mar 1997 10:40:34 -0500 Date: Thu, 13 Mar 1997 09:55:38 -0500 From: "Miller, Susan [PRI]" Subject: test To: "'chemistry@www.ccl.net'" Message-Id: Mime-Version: 1.0 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I am sending this message as a test to see if I can receive mail from CCL , since I got no messages from this group today (very strange). Susan From Vincent@averell.umh.ac.be Thu Mar 13 11:57:14 1997 Received: from averell.umh.ac.be for Vincent@averell.umh.ac.be by www.ccl.net (8.8.3/950822.1) id KAA11865; Thu, 13 Mar 1997 10:49:14 -0500 (EST) From: Received: by averell.umh.ac.be (AIX 3.2/UCB 5.64/4.03) id AA18831; Thu, 13 Mar 1997 16:41:45 +0100 Message-Id: <9703131541.AA18831@averell.umh.ac.be> Subject: Problem with NBO in G94 To: chemistry@www.ccl.net (CCL) Date: Thu, 13 Mar 1997 16:41:43 +0100 (NFT) X-Mailer: ELM [version 2.4 PL0] Content-Type: text Dear CCL members, I posted the following mail to the gaussian hotline, but may be the experience of the list members could be usefull. Dear Gaussian, I am triyng to perform a population analysis by mean of the NBO programm! My system is constituted of two polymer chains with a K or Rb atom in between. I am using the Gen keyword to define a DZVP basis. This is the keyword line: ># SVWN/GEN Density=Current Pop=NBO However, after the SCF calculation, the job continue, but whithout writing anymore in the .log file. The last informations are: > ************************Gaussian NBO Version 3.1************************* > N A T U R A L A T O M I C O R B I T A L A N D > N A T U R A L B O N D O R B I T A L A N A L Y S I S > ************************Gaussian NBO Version 3.1************************* > > Analyzing the SCF density > > Job title: NBO charges pour lpppeos+K, optimise > > Storage needed:****** in NPA,****** in NBO (8388608 available) and then nothing more; to stop the job, Ihave to kill it!! The same input line without the density keyword lead to the same feature. So the question is Did I make something wrong? Or is it due to the Gen keyword (other systems using the default keyword give the NBO calculation correctly)? Looking forward to hearing from you. Vincent Parente **************************************************************** * Vincent Parente * * Service de Chimie des Materiaux Nouveaux * * Center for Research in Molecular Electronics and Photonics * * University of Mons-Hainaut * * 20, Place du Parc, B-7000 Mons, BELGIUM * * tel : +32 65 37 3361 * * fax : +32 65 37 3366 * * +32 65 37 3054 * * e-mail : Vincent@averell.umh.ac.be * * http://morris.umh.ac.be/ * * http://morris.umh.ac.be/Vincent/vince.htm * **************************************************************** From jkong@clark.isrv.com Thu Mar 13 13:29:07 1997 Received: from clark.isrv.com for jkong@clark.isrv.com by www.ccl.net (8.8.3/950822.1) id MAA12986; Thu, 13 Mar 1997 12:34:34 -0500 (EST) Received: from localhost (jkong@localhost) by clark.isrv.com (8.7.3/8.7.3) with SMTP id MAA09367 for ; Thu, 13 Mar 1997 12:29:51 -0500 (EST) Date: Thu, 13 Mar 1997 12:29:50 -0500 (EST) From: "J. Kong" To: chemistry@www.ccl.net Subject: Wanted hard-to-converge SCF jobs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, We recently deviced some different ways to make the SCF (DFT and HF) converge easier. We are looking for real-world molecules which are hard to converge. Thank you in advance. Jing From ponder@dasher.wustl.edu Thu Mar 13 13:45:47 1997 Received: from dasher.wustl.edu for ponder@dasher.wustl.edu by www.ccl.net (8.8.3/950822.1) id MAA13110; Thu, 13 Mar 1997 12:52:05 -0500 (EST) From: Received: from localhost by dasher.wustl.edu (5.65v3.2/1.1.10.5/12Feb97-1108AM) id AA06289; Thu, 13 Mar 1997 11:51:17 -0600 Message-Id: <9703131751.AA06289@dasher.wustl.edu> Reply-To: ponder@dasher.wustl.edu To: ahocquet@cec.uchile.cl Cc: ponder@dasher.wustl.edu, chemistry@www.ccl.net Subject: RE: CCL:the MM2 (big) family Date: Thu, 13 Mar 97 11:51:17 -0600 X-Mts: smtp Dear Alexandre Hocquet, I can tell you something about one "family" of MM2 versions. The code distributed as "MM2" in the Chem3D package is actually my code written completely from scratch and based on MM2 circa 1987. It is IDENTICAL to "real" MM2 in all basic functional forms with the following exceptions: (1) It adds a quartic term to the bond stretch (just the next term in the Taylor expansion of the Morse potential, "real" MM2 uses the first two, harmonic and cubic, while we added the quartic). This has essentially no effect on minimum energy structures and energies (often less than 0.0001 kcal difference), but was added to make molecular dynamics stable, exp. at high temperature. Allinger's group has added this same term to MM3. (2) Our "MM2" uses the identical dipole-dipole term to real "MM2", but it also allows (in addition) use of partial charges (needed, for example to get the correct formal charge on a carboxylate, etc.). Then our code actually does electrostatics as a sum of the dipole-dipole, charge-charge and charge-dipole interactions. Again this same mechanism was subsequently implemented in MM3. (3) Our code uses a "hybrid" method for conjugated systems that is somewhat intermediate between the old MMPI and "real" MMP2. We use a straight PPP MO method instead of the "variable electroneg" style method, and we have calibrated the internal parameters to give good results on a number of kinds of heterocycles. The overall differences in results from MMP2 are small, but not zero. (4) Our code does not implement any of the special "parameter tweaking" terms that are in MM3 and in some versions of MM2, things like the electronegativity effect, anomeric effect, Bohlmann effect, etc. A later version of our MM2 (as well as an MM3 semi-clone) is available in the free molecular mechanics/dynamics package TINKER, which can be obtained with source code from http://dasher.wustl.edu/tinker. We have added many, many other options, parameter sets, etc., but it is possible to get TINKER to give a pretty authentic rendition of MM2 by turning off the bells and whistles. Hope this helps, Jay Ponder -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ From duanx@Picard.ml.wpafb.af.mil Thu Mar 13 14:29:11 1997 Received: from nsrhost.ml.wpafb.af.mil for duanx@Picard.ml.wpafb.af.mil by www.ccl.net (8.8.3/950822.1) id OAA13588; Thu, 13 Mar 1997 14:02:38 -0500 (EST) Received: from Picard.ml.wpafb.af.mil by nsrhost.ml.wpafb.af.mil with SMTP (1.39.111.2/16.2) id AA142519549; Thu, 13 Mar 1997 13:59:09 -0500 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA02733; Thu, 13 Mar 97 14:02:37 EST Date: Thu, 13 Mar 1997 14:02:36 -0500 (EST) From: Xiaofeng Duan To: chemistry@www.ccl.net Subject: help: mopac polymer calculation Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all: I am new in using MOPAC. I was trying to us it to calculate the band structures for the polymer system I am working with. Unfortunately, even I tried both mopac6 and mopac93, the results look not right because instead of curves I got straight lines for all the bands, i.e.,, at each k point, the energy is exactly the same for each band. Then I tried to use the example input file, polyethylene, from mopac manual, still I got straight lines for all the bands. I attached the polyethylene file here, hopefully someone can help me find the problem. Thanks in advance! *************************************** AM1 K=(0.01,6) T=20000 POLYETHYLENE, CLUSTER UNIT : C6H12 C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.540714 1 0.000000 0 0.000000 0 1 0 0 C 1.542585 1 113.532306 1 0.000000 0 2 1 0 C 1.542988 1 113.373490 1 179.823613 1 3 2 1 C 1.545151 1 113.447508 1 179.811764 1 4 3 2 C 1.541777 1 113.859804 1 -179.862648 1 5 4 3 XX 1.542344 1 108.897076 1 -179.732346 1 6 5 4 XX 1.540749 1 108.360151 1 -178.950271 1 7 6 5 H 1.114786 1 90.070026 1 126.747447 1 1 3 2 H 1.114512 1 90.053136 1 -127.134856 1 1 3 2 H 1.114687 1 90.032722 1 126.717889 1 2 4 3 H 1.114748 1 89.975504 1 -127.034513 1 2 4 3 H 1.114474 1 90.063308 1 126.681098 1 3 5 4 H 1.114433 1 89.915262 1 -126.931090 1 3 5 4 H 1.114308 1 90.028131 1 127.007845 1 4 6 5 H 1.114434 1 90.189506 1 -126.759550 1 4 6 5 H 1.114534 1 88.522263 1 127.041363 1 5 7 6 H 1.114557 1 88.707407 1 -126.716355 1 5 7 6 H 1.114734 1 90.638631 1 127.793055 1 6 8 7 H 1.115150 1 91.747016 1 -126.187496 1 6 8 7 Tv 7.746928 1 0.000000 0 0.000000 0 1 7 8 0 0 **************************************** Xiaofeng Duan, Ph. D. WL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 (513)255-9164 duanx@Picard.ml.wpafb.af.mil **************************************** From iainm@iainm.demon.co.uk Thu Mar 13 21:29:10 1997 Received: from relay-7.mail.demon.net for iainm@iainm.demon.co.uk by www.ccl.net (8.8.3/950822.1) id UAA16081; Thu, 13 Mar 1997 20:42:29 -0500 (EST) Received: from iainm.demon.co.uk ([158.152.30.61]) by relay-5.mail.demon.net id aa0509077; 13 Mar 97 23:48 GMT Message-ID: Date: Thu, 13 Mar 1997 23:47:29 +0000 To: chemistry@www.ccl.net From: Iain M McLay Subject: What is a good screening conc. for HTS MIME-Version: 1.0 X-Mailer: Turnpike Version 3.01 I hope you don't mind me using the CCL to ask this question, I believe that many readers working in the pharmaceutical industry may be asking themselves this question and I would like to see if there is some kind of industry consensus. In my company, Rhone Poulenc Rorer UK, we are often involved in a fascinating debate as to whether it is worth screening at high micromolar concentrations or not for a receptor antagonist. The argument against goes something like "a high micromolar lead is likely to be non-specific and very difficult to turn into a nanomolar final compound, we are making life hard for ourselves so screen at <10micromolar" The argument in favour goes something like "as long as the compound is competitive and reversible there is no reason why this cannot be turned rapidly into a nanomolar compound. Some targets are very difficult to find leads for and we cannot risk missing anything, so screen at >30micromolar" We are often told Pfizer never screens at more than 1micromolar or Glaxo always screens at 40micromolar, what is the truth. At my centre we have used both approaches depending on the beliefs of the project controllers, does this happen with other companies? For now I'll resist stating my own opinion as it might effect the debate. Thanks, Iain Iain M McLay e-mail iain@iainm.demon.co.uk From gabrielb@MIT.EDU Thu Mar 13 22:29:10 1997 Received: from MIT.EDU for gabrielb@MIT.EDU by www.ccl.net (8.8.3/950822.1) id WAA16371; Thu, 13 Mar 1997 22:00:19 -0500 (EST) From: Received: from CARBONARA.MIT.EDU by MIT.EDU with SMTP id AA07110; Thu, 13 Mar 97 22:00:11 EST Received: by carbonara.MIT.EDU (5.57/4.7) id AA17539; Thu, 13 Mar 97 22:00:15 -0500 Date: Thu, 13 Mar 97 22:00:15 -0500 Message-Id: <9703140300.AA17539@carbonara.MIT.EDU> To: chemistry@www.ccl.net Subject: How good is CHARMM for ligand design? Dear netters: I'll preface this question by stating that I know next to nothing about the field of computer-assisted ligand design, hence what follows will probably strike those with more experience as incredibly naive. The other day I attended a talk in which a couple of algorithms for the computer-assisted design of protein ligands were presented. The talk was very interesting, but I was surprised by the speaker's implicit standard for the algorithms' success being their ability to quickly find ligands with low Kd according to CHARMM (and the further implication that this was adequately representative of what should be expected experimentally); there was practically no mention of performance against experimental data. I was left wondering whether CHARMM is much better at predicting (small) ligand binding properties than I knew. Does anyone know of a recent critical review of CHARMM's success at discriminating good from bad protein ligands? Thanks in advance, GB gabrielb@athena.mit.edu