From chemistry-request@www.ccl.net Thu Jan 28 03:08:27 1999 Received: from condon.pc.Uni-Koeln.DE (condon.pc.Uni-Koeln.DE [134.95.49.84]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA17224 Thu, 28 Jan 1999 03:08:26 -0500 (EST) Received: by condon.pc.Uni-Koeln.DE; id AA25125; Thu, 28 Jan 1999 09:08:22 +0100 Date: Thu, 28 Jan 1999 09:08:22 +0100 (MET) From: Klaus-Peter Geigle To: computational chemistry list Subject: CIS-calculations - order of lowest electronic states Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hello everybody, in my CIS-calculations of aromatic hydrocarbons the Lb state is found to be the second excited (S2) state although this is spectroscopically wrong and higher level calculations (MCSCF) find the correct order for example in the case of naphthalene. In literature I found some examples similar to my results, but up to now no reason why CIS does not get the configuration interaction strong enough. Is there anybody who knows about this problem or a suitable reference? Thanks, KP *************************************************************************** Klaus Peter Geigle Tel.: ++49-221-470-4544 Phys. Chemie II Uni Koeln Fax.: ++49-221-470-5144 Luxemburger Str. 116 e-mail: K.P.Geigle@uni-koeln.de 50939 Koeln, Germany *************************************************************************** From chemistry-request@www.ccl.net Thu Jan 28 03:32:33 1999 Received: from chu1.chem.nthu.edu.tw (Chu1.Chem.nthu.edu.tw [140.114.45.236]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA17356 Thu, 28 Jan 1999 03:31:42 -0500 (EST) Received: by chu1.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA18401; Thu, 28 Jan 1999 16:25:47 +0800 From: hyl@chu1.chem.nthu.edu.tw (Hsin-Yi Liao) Message-Id: <9901280825.AA18401@chu1.chem.nthu.edu.tw> Subject: potential in G94 To: chemistry@www.ccl.net Date: Thu, 28 Jan 99 16:25:46 TAIST X-Mailer: ELM [version 2.4dev PL17] Dear netters, How can I get the most negative and positive value of molecular electrostatic potential in GAUSSIAN 94? Any reply will be appreciated. Regards, Hi-Ya Lai **************************************************** Dep. of Chemistry, NTHU, Hsin-Chu, Twiwan, ROC E-mail add.:hyl@chu1.chem.nthu.edu.tw hyl@chu.chem.nthu.edu.tw **************************************************** From chemistry-request@www.ccl.net Thu Jan 28 08:02:24 1999 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA18270 Thu, 28 Jan 1999 08:02:23 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with ESMTP id OAA08254 for ; Thu, 28 Jan 1999 14:03:16 +0100 (MET) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with SMTP id NAA01227 for ; Thu, 28 Jan 1999 13:59:15 +0100 (MET) Received: by styx.bruyeres.cea.fr (CEANET-1.1+) id AA06722; Thu, 28 Jan 1999 14:02:19 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by styx via smap id sma006697; Thu Jan 28 14:02:07 1999 Received: from ripault.cea.fr (manse.ripault.cea.fr [132.165.32.9]) by ripault.cea.fr. (8.8.7/8.7.3) with ESMTP id OAA16570 for ; Thu, 28 Jan 1999 14:01:40 +0100 Received: from manse.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.7/8.8.7) with SMTP id OAA02335 for ; Thu, 28 Jan 1999 14:02:31 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <36B05FE5.183C8837@ripault.cea.fr> Date: Thu, 28 Jan 1999 13:02:30 +0000 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.32 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: SUMMARY: DFT & H-bonds Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Hi, Many people asked me to summarize the replies to my question concerning the performance of DFT, and especially early functionals such as Becke-Perdew86, with regard to the description of the energetic of H-bonds. Much work appears to have been done on this subject as I got a lot of references (Don't ask me already about their content, first I have to plan a trip to Paris to get them... The "decentralisation" is not yet effective with regard to libraries -). Clearly, everybody agree that hybrid functionals are better than GGA functionals, the latter being themselves much better than LDA. Recently, the team by Salahub has developped a LAP functional which performs well. Somebody also pointed to the need for extended basis sets for convergence. With regard to the performance of early functionals, I retain from the answers that the results provided by functonals such as BP for weak bonds are fairly erratic. Finally, in view of the wealth of answers pointing to new functionals, especially hybrid ones, BP appears old-fashioned. In fact, we used this functional for the sake of comparison with previous work, where we replaced BP geometries with molecular mechanics MMFF structures. Regards -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From chemistry-request@www.ccl.net Wed Jan 27 03:26:48 1999 Received: from euler.central.cranfield.ac.uk (euler.central.cranfield.ac.uk [138.250.48.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA06853 Wed, 27 Jan 1999 03:26:47 -0500 (EST) Received: from btmodelling.pc.cranfield.ac.uk ([138.250.75.1] helo=btmodelling) by euler.central.cranfield.ac.uk with smtp (Exim 1.92 #2) for CHEMISTRY@www.ccl.net id 105QJE-0005wm-00; Wed, 27 Jan 1999 08:26:48 +0000 Message-Id: <3.0.3.32.19990127082322.009fdd30@mailboxes.ccc.cranfield.ac.uk> X-Sender: bi0100@mailboxes.ccc.cranfield.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 27 Jan 1999 08:23:22 +0000 To: CHEMISTRY@www.ccl.net From: Richard M Day Subject: Energy Minimisation of Proteins in vacuo Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi CCL'ers, I have been trying for a while to refine a protein structure (from a PDB !) and try and remove the problems of poor dihedrals (not just due to function), poor bond lengths, iffy sidechain planarity etc so it can be used to do rational design, de novo design etc etc. Now the protein I have to work on is 70Kda or so and to try and do this work using a solvated model would be fairly mad because I would have to buy a few extra hard drives for my indy to process it with a newton raphson type algorithm. The alternative in literature suggests in vacuo simulations using energy minimisation (DISCOVER, CHARMM, MAXIMIN whatever) with a variable dielectric-distance function and with a fiddle factor dielectric (different authors reckon either 4 or 20). I tried all these with my protein and it seems to work a lot better at 20 rather than 1 - and according to the Vriend & Sander WHAT_CHECK for proteins the dihedrals (according to ramachandran) seem to have become more tightly focussed where they should be and the side chains more planar, bond lengths seem to be more like the norm. Is this a good alternative to solvation or does this technique completely over-refine the model and make it worse that just using the raw data ? Any comment would be greatly appreciated, summary as usual. Best Wishes, Richard Day. Cranfield Biotechnology Centre, +44 1234 750111 x3562 From chemistry-request@www.ccl.net Wed Jan 27 05:04:13 1999 Received: from mailhost.tue.nl (mailhost.tue.nl [131.155.2.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA07181 Wed, 27 Jan 1999 05:04:10 -0500 (EST) Received: from sg10.chem.tue.nl [131.155.80.53] by mailhost.tue.nl (8.9.0) for id LAA08839 (ESMTP). Wed, 27 Jan 1999 11:04:07 +0100 (MET) Received: from tgakrh@localhost by sg10.chem.tue.nl (8.8.5) for chemistry@www.ccl.net id LAA05878. Wed, 27 Jan 1999 11:04:06 +0100 (MET) From: Roelant Harmsen Message-Id: <199901271004.LAA05878@sg10.chem.tue.nl> Subject: UV/Vis calculations To: chemistry@www.ccl.net Date: Wed, 27 Jan 1999 11:04:06 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Hi All, Does anyone know of a program that calculates UV/VIS spectra? And is it theoretically possible to do it with DFT? Cheers, Roelant ********************************************************************** Roelant Harmsen |tel: ++31 40 2473575/5032 University of Technology Eindhoven |fax: ++31 40 2455054 Schuit Institute of Catalysis |e-mail: R.J.Harmsen@tue.nl P.O. box 513 |e-mail : tgakrh@chem.tue.nl 5600 MB Eindhoven | The Netherlands |AD&D: Xahnar (Wild Mage) Homepage: http://www.tak.chem.tue.nl/personal/rharmsen ********************************************************************** From chemistry-request@www.ccl.net Wed Jan 27 07:26:12 1999 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA07744 Wed, 27 Jan 1999 07:26:04 -0500 (EST) Received: from localhost (jan@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id NAA21534 for ; Wed, 27 Jan 1999 13:25:37 +0100 Date: Wed, 27 Jan 1999 13:25:37 +0100 (NFT) From: Jan De Kerpel To: CHEMISTRY@www.ccl.net Subject: CLL: academic docking software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL's, I am looking for receptor/ligand protein docking software (flexible and/or rigid) like FlexiDock or Affinity (provided by some commercial groups) but for low/free prices (academic usage). To be run on sgi R10000, IBM RS6000 or pc. Thanks, Jan De Kerpel email : jan.dekerpel@chem.kuleuven.ac.be ************************************************************* Labo Quantumchemistry Celestijnenlaan 200F Departement of Chemistry 3001 Leuven (Heverlee) Katholieke Universiteit Leuven BELGIUM tel : 32 16 327393 fax : 32 16 327992 email : jan.dekerpel@chem.kuleuven.ac.be ************************************************************* From chemistry-request@www.ccl.net Wed Jan 27 07:50:35 1999 Received: from hotmail.com (law-f126.hotmail.com [209.185.131.189]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA07891 Wed, 27 Jan 1999 07:50:31 -0500 (EST) Received: (qmail 9469 invoked by uid 0); 27 Jan 1999 12:49:52 -0000 Message-ID: <19990127124952.9468.qmail@hotmail.com> Received: from 199.89.234.120 by www.hotmail.com with HTTP; Wed, 27 Jan 1999 04:49:51 PST X-Originating-IP: [199.89.234.120] From: "Gautham Nadig" To: chemistry@www.ccl.net Subject: HELP WITH TINKER Date: Wed, 27 Jan 1999 04:49:51 PST Mime-Version: 1.0 Content-Type: text/plain Hello, I am trying to implement TINKER to run MD on biomolecules. I am unable to do a minimization of a tripeptide in solution. the energy blows up. is there an example file where i could look into? [it is a tripeptide immersed in a 15A cube of tip3p waters]. the minimization in vaccum runs fine. minimization/md of water alone runs fine too. any help is greatly appreciated gautham -------- Monsanto,R&D center, Bangalore, INDIA ------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@www.ccl.net Wed Jan 27 11:33:43 1999 Received: from bobino.sefmedia.com (www.sefmedia.com [207.164.6.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA10005 Wed, 27 Jan 1999 11:33:42 -0500 (EST) Received: from ppp-5200-4737.mtl.total.net (ppp-5200-4737.mtl.total.net [205.205.77.99]) by bobino.sefmedia.com (NTMail 3.02.13) with ESMTP id ta018349 for ; Wed, 27 Jan 1999 11:33:39 -0500 Received: from [192.1.1.4] by foghorn.chemcomp.com (NTMail 3.03.0017/24.aaae) with ESMTP id oa004850 for ; Wed, 27 Jan 1999 11:21:47 -0500 Sender: chris@www.ccl.net Message-ID: <36AF3BD1.62B4@chemcomp.com> Date: Wed, 27 Jan 1999 11:16:17 -0500 From: Chris Williams Organization: ccgi X-Mailer: Mozilla 3.04 (X11; I; SunOS 5.3 sun4m) MIME-Version: 1.0 To: Florence Lebon CC: chemistry@www.ccl.net Subject: Re: CCL:superimpose References: <199901270808.JAA37834@spsrv.scf.fundp.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Dr. Lebon, The Chemical Computing Group software MOE (Molecular Operating Environment) offers a number of tools for multiple conformation alignments. Conformers can be superimposed based on either all atoms in the molecule, or based on a subset of atoms. There is no limit to the number of conformers that may be superimposed at one time (save hardware limitations). The MOE software is built on an embedded programming language (SVL) that allows for fast and easy modification and development of applications. Please visit the CCG website at http://www.chemcomp.com All the best, Chris Williams ---------------------------------- Chris Williams, Ph.D. Customer Support/Applications Scientist, Chemical Computing Group, Inc. 1255 University St., Suite 1600 Montreal, Quebec CANADA H3B 3X3 Tel: (514) 393-1055 Fax: (514) 874-9538 From chemistry-request@www.ccl.net Wed Jan 27 14:56:12 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA13934 Wed, 27 Jan 1999 14:56:11 -0500 (EST) Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id OAA27923 for ; Wed, 27 Jan 1999 14:56:10 -0500 (EST) Message-ID: Date: 27 Jan 1999 14:56:27 -0500 From: "Lipkowitz" Subject: Differential Free Energies To: "Comp Chem List" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear colleagues: I am writing an Accounts of Chemical Research article on computational studies of enantioselective binding. I've had some experiences determining differential free energies of binding in chromatographic systems as well as for host guest complexes involving cyclodextrins using MD and MC strategies but I tended to avoid Free Energy Perturbation (FEP) methods for a variety of reasons (I didn't think they could compute such small free energy differences between D and L enantiomers binding to a selector.... often DDG < kT). I have some published papers where D vs L enantiomer energy differences have been computed by FEPT but I would like to hear your opinions about FEP's validity for such calculations. Maybe I can find a group consensus about this to pass on to the Accounts readers. I'm especially interested in the industrial scientists at pharmaceutical companies who no doubt have reams of unpublished results about D/L drug binding. Kenny Lipkowitz From chemistry-request@www.ccl.net Wed Jan 27 17:04:03 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA14829 Wed, 27 Jan 1999 17:04:00 -0500 (EST) Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id XAA35973; Wed, 27 Jan 1999 23:02:38 +0100 ("MET) Date: Wed, 27 Jan 1999 23:02:37 +0100 From: Christian Pilger To: Jan De Kerpel cc: chemistry@www.ccl.net Subject: Re: CCL:academic docking software In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Jan, > I am looking for receptor/ligand protein docking software > (flexible and/or rigid) like FlexiDock or Affinity (provided > by some commercial groups) but for low/free prices (academic > usage). > To be run on sgi R10000, IBM RS6000 or pc. > > Thanks, > Jan De Kerpel > email : jan.dekerpel@chem.kuleuven.ac.be you should take a look at the following URL: http://www.scripps.edu/pub/olson-web/doc/autodock/ I got good results (compared to X-ray) employing autodock. I used the software on SGI, SUN, and LINUX. Regards, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- > > ************************************************************* > > Labo Quantumchemistry Celestijnenlaan 200F > Departement of Chemistry 3001 Leuven (Heverlee) > Katholieke Universiteit Leuven BELGIUM > > tel : 32 16 327393 > fax : 32 16 327992 > > email : jan.dekerpel@chem.kuleuven.ac.be > > ************************************************************* > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 chemistry-request@www.ccl.net Wed Jan 27 21:20:07 1999 Received: from sungod.ccs.yorku.ca (Ijnw78lasSVDWZY4DO7EbidhLl6PW5Mx@sungod.ccs.yorku.ca [130.63.236.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA15934 Wed, 27 Jan 1999 21:20:06 -0500 (EST) Received: from mountain.chem.yorku.ca (mountain.chem.yorku.ca [130.63.133.28]) by sungod.ccs.yorku.ca (8.8.7/8.6.11) with ESMTP id VAA07194 for ; Wed, 27 Jan 1999 21:20:07 -0500 (EST) Received: from localhost (waito@localhost) by mountain.chem.yorku.ca (8.8.4/8.6.12) with SMTP id VAA13629 for ; Wed, 27 Jan 1999 21:17:53 -0500 (EST) Date: Wed, 27 Jan 1999 21:17:53 -0500 (EST) From: Wai-To Chan To: chemistry@www.ccl.net Subject: Visualisation program suggestion Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues, I am writing this note to solicit your comments on any appropriate visualization package for developing molecular graphics applications on a SGI workstation. I am looking for a program that can extract from a cubic grid of various electron density properties (computed from Gaussian using the cube option) these features: 2D and 3D contour plots 3D multi-isovalued surfaces gradient vectors (in 2D and 3D space) Locations of maxima and minima Specifically the program must enable me to produce an isovalued electron-density surface. The program also must put out the cartesian coordinates of this surface which I will need for subsequent evaluation of other quantities on this surface. At present I have in my mind either AVS (advanced visualization system) or Iris explorer. Can someone comment on these two programs particularly? My primiary considerations are prices, user-friendliness, flexiblity and popularity among computational chemists. Any suggestion of freeware would be very useful although I've not been able to find one free program that meets all my needs. Other than modular graphics package an easy-to-program graphics subroutine library (compatible with C if not FORTRAN) would also be helpful. Thanks. Wai-To Chan Department of Chemistry York University, Toronto Ontario, Canada email: wtchan@yorku.ca From chemistry-request@www.ccl.net Thu Jan 28 15:58:47 1999 Received: from chemvx.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA22867 Thu, 28 Jan 1999 15:58:47 -0500 (EST) Received: from biosym.chem.tamu.edu ([165.91.176.9]) by chemvx.chem.tamu.edu (Netscape Mail Server v2.02) with SMTP id AAA144 for ; Thu, 28 Jan 1999 15:00:52 -0600 Sender: plin@mail.chem.tamu.edu (Ping Lin) Message-ID: <36B0CF88.41C6@mail.chem.tamu.edu> Date: Thu, 28 Jan 1999 12:58:48 -0800 From: ping lin Organization: Texas A&M University X-Mailer: Mozilla 2.0S (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL: programs for electron transfer theory X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, everyone, I am looking for any programs or softwares that is used in electron transfer study. There have been many models developed in electron transfer theory. I want to do some quantum mechanical study in some systems. Any suggestion is welcomed. Thanks, Ping Lin Texas A&M University plin@mail.chem.tamu.edu