From chemistry-request@server.ccl.net Thu Feb 3 00:11:33 2000 Received: from goshen.rutgers.edu (goshen.rutgers.edu [165.230.180.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA31577 for ; Thu, 3 Feb 2000 00:11:32 -0500 Received: from email.eden.rutgers.edu (arcpc38.rutgers.edu [128.6.83.48]) by goshen.rutgers.edu (8.8.8/8.8.8) with ESMTP id XAA27598 for ; Wed, 2 Feb 2000 23:06:13 -0500 (EST) Message-ID: <3898FE79.7D6A9E91@email.eden.rutgers.edu> Date: Wed, 02 Feb 2000 23:05:13 -0500 From: jianquan Organization: Rutgers University X-Mailer: Mozilla 4.61 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: pol_h Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hi, I can't access to AMBER software? Does sb. know if pol_h, a program to add polar hydrogen, is a free or share software? And if yes, Can you tell me how to download it? Thanks in advance. jianquan From chemistry-request@server.ccl.net Wed Feb 2 18:17:36 2000 Received: from yogi.pc1.uni-duesseldorf.de (root@yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA30239 for ; Wed, 2 Feb 2000 18:17:35 -0500 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id XAA00899; Wed, 2 Feb 2000 23:12:14 +0100 From: "Jochen Küpper" MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14488.43964.359663.199082@yogi.pc1.uni-duesseldorf.de> Date: Wed, 2 Feb 2000 23:12:12 +0100 (CET) To: Peter Shenkin Cc: chemistry@ccl.net Subject: CCL:Swap Space on Unix In-Reply-To: References: <3.0.6.32.20000202110142.00935b90@chem.boisestate.edu> X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id SAA30240 Peter Shenkin writes: > Well, if the jobs are really swapping then you will probably > be greatly slowed down by this strategy, but it ought to be > harmless from a system point of view. Yep, but you really have to stress that Gaussian's out-of-memory algorithms are better fopr Gaussian than the generic OS demand paging. > There is also a way to configure DECs to "overcommit" virtual > memory. Yes, sometimes very usefull. > I don't know whether G98 is careful never to allocate more > memory than it needs, but if it sometimes does allocate > more than it actually uses, configuring your OS this way > would be another way to go. Me too, but my jobs usually have an RSS close to size at one point, so I guess it uses all the allocated memory (at least within my applications). > BTW, your Subject: refers to a UNIX question, but in fact > the answer differs for different flavors of UNIX. The above > is correct for TRU64, AFAIK. Yep. Some *nices do overcommitment by default, others need to be configured that way (like Tru64). Is therone out that doesn't do it at all - I assume not. Jochen -- Heinrich-Heine-Universität Institut für Physikalische Chemie I Jochen Küpper Universitätsstr. 1, Geb. 26.43.02.29 40225 Düsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.jochen-kuepper.de From chemistry-request@server.ccl.net Wed Feb 2 19:00:36 2000 Received: from watson.bcm.tmc.edu (bcm.tmc.edu [128.249.2.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA30419; Wed, 2 Feb 2000 19:00:35 -0500 Received: from bcm.tmc.edu (njing.phys.bcm.tmc.edu [128.249.82.231]) by watson.bcm.tmc.edu (8.8.8/8.8.8) with ESMTP id QAA21163; Wed, 2 Feb 2000 16:55:24 -0600 (CST) Sender: jliu@bcm.tmc.edu Message-ID: <3898536F.C2743ADB@bcm.tmc.edu> Date: Wed, 02 Feb 2000 16:55:27 +0100 From: Jie Liu X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, chemistry-request@server.ccl.net Subject: About autodock3 Content-Type: multipart/alternative; boundary="------------76A740340BC355BB7F708DC4" --------------76A740340BC355BB7F708DC4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers: I docked a ligand (oligonucleotide with 523 atoms) into the protein by using Autodock3.0.2.When I executed " autodock3 -p name.dpf -l name.dlg &", Autodock3 can not complete the task successfully. It gave me following information: *autodock3: ERROR: ERROR: 523 records read in, but only dimensioned for 512. *Change "MAX_RECORDS" in "constants.h". *autodock3: Aborting... *autodock3: Unsuccessful Completion. I ever tried to incerease the grid map dimensions of the ligand, but the problem still existed. Does it mean that this program can not work on ligand with more than 512 atoms or I should modify some parameters of the program?How can I modify the parameters?Thanks a lot for any advices. Best regards, Jie Liu -- Jie Liu, Ph.D. Department of Molecular Physiology and Biophysics Baylor College of Medicine Houston, TX 77030 USA --------------76A740340BC355BB7F708DC4 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers:
        I docked a ligand (oligonucleotide with 523 atoms) into the protein by using Autodock3.0.2.When I executed " autodock3 -p name.dpf -l name.dlg &", Autodock3 can not complete the task successfully. It gave me following information:
 
  • autodock3: ERROR: ERROR: 523 records read in, but only dimensioned for 512.
  • Change "MAX_RECORDS" in "constants.h".
  • autodock3: Aborting...
  • autodock3: Unsuccessful Completion.

    •         I ever tried to incerease the  grid map dimensions of the ligand, but the problem still existed.
            Does it mean that this program can not work on ligand with more than 512 atoms or I should modify some parameters of the program?How can I modify the parameters?Thanks a lot for any advices.

    Best regards,

    Jie Liu
     

    --
    Jie Liu, Ph.D.
    Department of Molecular Physiology and Biophysics
    Baylor College of Medicine
    Houston, TX 77030
    USA

      --------------76A740340BC355BB7F708DC4-- From chemistry-request@server.ccl.net Thu Feb 3 01:14:11 2000 Received: from igor.wag.caltech.edu (igor.wag.caltech.edu [131.215.33.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA31988 for ; Thu, 3 Feb 2000 01:14:11 -0500 Received: from wag.caltech.edu (charter-185-237.caltech.edu [131.215.185.237]) by igor.wag.caltech.edu (8.9.3/8.9.3) with ESMTP id VAA586898 for ; Wed, 2 Feb 2000 21:08:50 -0800 (PST) Sender: rpm@wag.caltech.edu Message-ID: <3898E38C.B4A0A2BD@wag.caltech.edu> Date: Wed, 02 Feb 2000 21:10:20 -0500 From: "Richard P. Muller" X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.6-15apmac ppc) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: CCL: Nuclear Attraction Integrals References: <200002022112.WAA13134@sg1503.chemie.uni-marburg.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Can someone point me to references on the computation of nuclear attraction integrals using Gaussian Basis Functions. Thanks in advance, Rick rpm@wag.caltech.edu From chemistry-request@server.ccl.net Thu Feb 3 04:48:20 2000 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.64.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA00206 for ; Thu, 3 Feb 2000 04:48:20 -0500 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 27053 invoked from network); 3 Feb 2000 08:43:12 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 3 Feb 2000 08:43:12 -0000 Received: (qmail 4158 invoked by uid 10283); 3 Feb 2000 08:42:45 -0000 Message-ID: <20000203084245.4157.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re: CCL:Nuclear Attraction Integrals To: rpm@wag.caltech.edu (Richard P. Muller) Date: Thu, 3 Feb 100 09:42:45 +0100 (MET) Cc: chemistry@ccl.net In-Reply-To: <3898E38C.B4A0A2BD@wag.caltech.edu> from "Richard P. Muller" at Feb 2, 0 09:10:20 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit A nuclear attraction integral is just a special case of a two-electron integral: = (ij | kk) where k is a normalized s-Funktion centered at c with "infinitly high" exponent. Some simplifications arise naturally, so if you have a text on two-electron integrals, it also covers nuclear attr. integrals. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Thu Feb 3 04:55:07 2000 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.64.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA00269 for ; Thu, 3 Feb 2000 04:55:07 -0500 From: Christoph.van.Wuellen@ruhr-uni-bochum.de Received: (qmail 3119 invoked from network); 3 Feb 2000 08:49:59 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.64.2) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 3 Feb 2000 08:49:59 -0000 Received: (qmail 5327 invoked by uid 10283); 3 Feb 2000 08:49:32 -0000 Message-ID: <20000203084932.5326.qmail@sgi249.rz.ruhr-uni-bochum.de> Subject: Re, References on exact solutions ... To: chemistry@ccl.net Date: Thu, 3 Feb 100 09:49:32 +0100 (MET) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I wonder if during this discussion is has been pointed out that H2+ is a three-body system. The "exact" solution discussed so far is however the solution of a one-body Schroedinger equation with the clamped nuclei hamiltonian. ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Thu Feb 3 06:27:07 2000 Received: from angelos.phc.chalmers.se (angelos.phc.chalmers.se [129.16.97.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA00761 for ; Thu, 3 Feb 2000 06:27:05 -0500 Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by angelos.phc.chalmers.se (8.9.3/8.9.3) with ESMTP id LAA16163; Thu, 3 Feb 2000 11:21:42 +0100 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id LAA16995; Thu, 3 Feb 2000 11:21:42 +0100 Date: Thu, 3 Feb 2000 11:21:40 +0100 (MET) From: Harald Svedung To: help@gaussian.com cc: chemistry@server.ccl.net Subject: CO-He scan Omega strange Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Using g98 revA.6 and the following input to scan the coaxial CO-He interaction: %nproc=1 %mem=80000000 #RMP2/cc-pVTZ Scan ExtraBasis Test C-O - He scan r2 0 1 X1 X2 X1 r2 O1 X2 1. X1 90. C1 O1 r1 X2 90. X1 180. He1 X1 1. X2 90. O1 0. Variables: r2 1.66643212 30 0.166643212 r1 1.13896129 O C 0 AUG-cc-pVTZ **** , the Omega subrutine detects a 'Change in point group or standard orientation.' at an r2 distance of 3.499507 AA. The reported fraimwork group inside this distance is C*V[C*(COHe)] and at the failing point C*V[C*(HeOC)]. I cant se why this motivates a termination of the scan. ;-) Is there a fast workarround ? with regards :-) /Harald Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Thu Feb 3 07:39:49 2000 Received: from biol2.bio.nagoya-u.ac.jp ([133.6.127.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA01960 for ; Thu, 3 Feb 2000 07:39:48 -0500 Received: from [133.6.127.65] by biol2.bio.nagoya-u.ac.jp (8.8.8/1.1.22.3/26Dec99-0255AM) id UAA0000023836; Thu, 3 Feb 2000 20:35:23 +0900 (JST) Date: Thu, 3 Feb 2000 20:35:23 +0900 (JST) Message-Id: <200002031135.UAA0000023836@biol2.bio.nagoya-u.ac.jp> To: chemistry@ccl.net From: shinoda@biol2.bio.nagoya-u.ac.jp (Kazuki Shinoda) Subject: GTP parameters MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear CCLers, Does anyone has any information about Amber parameter set for GTP ? Any information will be appreciated. Best regards. Kazuki ================================================ Kazuki Shinoda, MC2 Division of Biological Science, Graduate school of Science Nagoya University, Chikusa, Nagoya 464-8602, Japan E-mail : shinoda@biol2.bio.nagoya-u.ac.jp URL: http://bio.nagoya-u.ac.jp:8001/~kazuki/kazuki.html ================================================ From chemistry-request@server.ccl.net Thu Feb 3 09:10:07 2000 Received: from prserv.net (out4.prserv.net [32.97.166.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA02333 for ; Thu, 3 Feb 2000 09:10:07 -0500 From: jmmckel@attglobal.net Received: from attglobal.net ([32.100.232.52]) by prserv.net (out4) with SMTP id <2000020313044523900m743ie>; Thu, 3 Feb 2000 13:04:45 +0000 Message-ID: <389939DA.C4EF362D@attglobal.net> Date: Thu, 03 Feb 2000 08:18:34 +0000 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.7 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Deconvolution Software Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! Can anyone point me to a fitting program that can deconvolute a UV/VIS spectral curve into gaussian, or other, components? Thanks! John McKelvey From chemistry-request@server.ccl.net Thu Feb 3 10:24:57 2000 Received: from ntsvexch.albmolecular.com (mail.albmolecular.com [205.247.153.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03187 for ; Thu, 3 Feb 2000 10:24:57 -0500 Received: by Ntsvexch with Internet Mail Service (5.5.2650.21) id <1D2CQTG9>; Thu, 3 Feb 2000 09:21:12 -0500 Message-ID: <80F79FF3ECD6D1119D9000805FCC602A82CCA2@Ntsvexch> From: "Andruski, Stephen W." To: "'CCL'" Subject: Re:Deconvolution Software Date: Thu, 3 Feb 2000 09:21:11 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain John McKelvey wrote: >>Can anyone point me to a fitting program that can deconvolute a UV/VIS >>spectral curve into gaussian, or other, components? I know that the plotting program "Origin" from Microcal can do this on the Windows platform. Steve Andruski > *********************************** > Dr. Stephen W. Andruski > Senior Research Chemist II > Albany Molecular Research, Inc. > 21 Corporate Circle > Albany, New York 12203 USA > Tel. (518) 464-0279, Ext. 2414 > Fax (518) 464-0289 > E-mail: stephena@albmolecular.com > http://www.albmolecular.com > ************************************ > > > > > > > From chemistry-request@server.ccl.net Thu Feb 3 11:03:14 2000 Received: from falcon.kvac.uu.se (falcon.kvac.uu.se [130.238.70.84]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03474 for ; Thu, 3 Feb 2000 11:03:14 -0500 Received: from wolf.kvac.uu.se (wolf.kvac.uu.se [130.238.70.83]) by falcon.kvac.uu.se (8.8.6/8.8.6) with SMTP id QAA17406 for <@falcon.kvac.uu.se:chemistry@ccl.net>; Thu, 3 Feb 2000 16:01:19 +0100 (CET) Received: by wolf.kvac.uu.se (950413.SGI.8.6.12/930416.SGI) for chemistry@ccl.net id QAA16511; Thu, 3 Feb 2000 16:01:18 +0100 From: "Yanni Wang" Message-Id: <10002031601.ZM16509@wolf.kvac.uu.se> Date: Thu, 3 Feb 2000 16:01:18 +0000 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: Solvent effect Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, I am trying to study the protein effect with gauss98. However I always get the same results as that in water. The following is my input file. Does anyone know how to solve it? Many thanks in advance! ******************************* #b3lyp/6-311g(2d,p) SCRF=(PCM,Read) bq in protein 0 1 C 1.266098 0.000000 -0.672636 C 1.266098 0.000000 0.672636 H 2.184912 0.000000 1.252450 O 0.000000 0.000000 2.668981 C -1.266098 0.000000 0.672636 H 2.184912 0.000000 -1.252450 C 0.000000 0.000000 1.439558 C 0.000000 0.000000 -1.439558 C -1.266098 0.000000 -0.672636 O 0.000000 0.000000 -2.668981 H -2.184912 0.000000 1.252450 H -2.184912 0.000000 -1.252450 4.0 -- ******************************************************************** Yanni Wang | Phone: +46 18 471 6840 Department of Quantum Chemistry | Fax: +46 18 50 24 02 Uppsala University | E-mail: wangyn@kvac.uu.se Box 518 S-751 20 Uppsala, Sweden From chemistry-request@server.ccl.net Thu Feb 3 11:03:25 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03486 for ; Thu, 3 Feb 2000 11:03:25 -0500 Received: from chem_mail.psc.sc.edu (mail.chem.sc.edu [129.252.151.17]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id JAA06688 for ; Thu, 3 Feb 2000 09:58:00 -0500 (EST) Received: from psc.sc.edu (killa.chem.sc.edu [129.252.151.213]) by chem_mail.psc.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id Z65J53KM; Thu, 3 Feb 2000 09:57:57 -0500 Message-ID: <389997F8.268BD1C7@psc.sc.edu> Date: Thu, 03 Feb 2000 10:00:19 -0500 From: Angelica Garcia-Zacarias Reply-To: cagz@psc.sc.edu Organization: University of South Carolina X-Mailer: Mozilla 4.7 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: G94 & Tru64 Unix Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear CCL's Has anyone ever experience problems to compile G94 under Compaq Tru64 UNIX? (For a Microway Screamer-LX 600 MHz 21164 CPU) Any advice will be appreciated Angelica -- ____________________________________________________________ Angelica G. Zacarias Chemistry and Biochemistry E-mail: cagz@psc.sc.edu University of South Carolina Phone: (803) 777 0720 Columbia, SC 29208 Fax: (803) 777 9521 ____________________________________________________________ Happiness is a conscious choice, not an automatic response. -- Mildred Barthel ____________________________________________________________ From chemistry-request@server.ccl.net Thu Feb 3 12:24:11 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA03966 for ; Thu, 3 Feb 2000 12:24:11 -0500 Received: from icream3 (icream3 [128.227.192.183]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id LAA29887; Thu, 3 Feb 2000 11:18:44 -0500 (EST) Message-Id: <200002031618.LAA29887@qtp.ufl.edu> Date: Thu, 3 Feb 2000 11:18:43 -0500 (EST) From: Stefan Fau Reply-To: Stefan Fau Subject: Re: CCL:CO-He scan Omega strange To: svedung@phc.chalmers.se Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: OKbiA5o3r20n54pFBwhayw== X-Mailer: dtmail 1.3.0 CDE Version 1.3 SunOS 5.7 i86pc i386 Hi Harald, AFAIK the only cure to that problem is to turn off symmetry which makes your calculation more costly. I would just restart the calculation with the geometry the caused the "change in pointgroup" problem. Concerning the problems this change in pointgroup might cause, I wonder if C*V[C*(HeOC)] and C*V[C*(COHe)] indicate different orientations with respect to the z-axis, i.e. the He atom pointing to + and - z. (Can be checked by looking at the "Standard orientation".) If that is the case, you may have trouble with any data from the previous geometry that are to be reused for this geometry _and_ are based on cartesian coordinates. Stefan ______________________________________________________________________ Dr. Stefan Fau fau@qtp.ufl.edu Quantum Theory Project University of Florida Gainesville FL 32611-8435 From chemistry-request@server.ccl.net Thu Feb 3 12:52:30 2000 Received: from aorta.physiome.com (mail.physiome.com [204.142.61.124]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04133 for ; Thu, 3 Feb 2000 12:52:29 -0500 Received: from COMPCHEM ([192.168.1.67]) by aorta.physiome.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0) id 1BRPMR6Q; Thu, 3 Feb 2000 11:46:02 -0500 Message-ID: <00bb01bf6e67$8263ab00$4301a8c0@physiome.com> From: "Roberta Susnow" To: Subject: Summary of QSAR review responses. Date: Thu, 3 Feb 2000 11:55:43 -0500 Hi, Below is a compilation of all the responses I received regarding the QSAR review. It's pretty long! Thanks for all your input. Roberta Susnow Physiome Sciences 1)If you are interested in physical property and environmental fate (e.g., biodegradability, atmospheric oxidation) QSARs, a good review is P.H. Howard and W.M. Meylan. Prediction of Physical Properties, Transport, and Degradation for Environmental Fate and Exposure Assessments. pp 185-205. In: Quantitative Structure-Activity Relationships in Environmental Sciences - VII, Proc.QSAR96. Ed. F. Chen and G. Schuurmann. SETAC Press, Pensacola, FL. 1997. Phil Philip H. Howard, Ph.D. Phone: 315-452-8417 Director Fax: 315-452-8440 Environmental Science Center Email: howardp@syrres.com Syracuse Research Corporation Website http://esc.syrres.com/ 6225 Running Ridge Rd. North Syracuse, NY 13212 2)In addition to the reviews I have written a book which is a practical guide to the methods (including set design) so that might be some help. The book is: "Data Analysis for Chemists: Application to QSAR and Chemical Product Design" Oxford University Press, 1995, ISBN 0 19 855728 0. and some book chapters are: "Quantitative Structure Activity Relationships" in "Similarity Models in Chemistry, Biochemistry and Related Fields", T.M. Krygowski, J. Shorter and R. Zalewski (Eds), pp 557-627, Elsevier, Amsterdam, 1991. "Pattern Recognition Methods for use in Rational Drug Design" in "Molecular Design and Modeling: Concepts and Applications", J.J. Langone (Ed.), Vol. 203 of Methods in Enzymology, Academic Press, 1991 pp 613-638. "Neural Networks - A Tool for Drug Design" with D.T. Manallack in "Advanced Computer-Assisted techniques in Drug Discovery", volume 3 of "Methods and Principles in Medicinal Chemistry", H. van de Waterbeemd (Ed.), VCH, Weinheim, New York, 1994 pp 293-318. "Neural Networks in the Search for Similarity and Structure-Activity" with D.W. Salt in "Molecular Similarity Tools for Drug Design", P.M. Dean (Ed.), Blackie Academic and Professional, London, Glasgow, 1995 pp 187-214. "Electronic Structure Calculations in Quantitative Structure Property Relationships" with M.R. Saunders in Volume 1 of "Advances in Quantitative Structure Property Relationships", M. Charton (Ed.), JAI Press, Greenwich, London, 1996, pp 53-79. "Structure-Property Correlations in Molecular Design" in "Structure-Property Correlations in Drug Research", H. van de Waterbeemd (Ed.), R.G. Landes, Austin, USA, 1996, pp 81-110. A couple of very recent reviews are: "Neural Networks in Drug Discovery; Have they Lived up to Their Promise ?" D.T. Manallack and D.J. Livingstone, Eur. J. Med. Chem., 34, 195-208 (1999). "The Characterization of Chemical Structures Using Molecular Properties. A Survey" D.J. Livingstone, J. Chem. Inf. Comput. Sci., in press. I hope this helps, happy reading ! David L. ------------------------------------------------------------------ D.J. Livingstone ChemQuest Delamere House, 1 Royal Crescent, Sandown. Isle of Wight UK PO36 8LZ Phone & Fax: +44 (0)1983 401793 e-mail davel@chmqst.demon.co.uk http://www.chmqst.demon.co.uk ------------------------------------------------------------------ 3)It may be hard to get anything very current as the field is undergoing rapid evolution. My work with Frank Burden is exploring all these issues with a view to developing a very robust QSAR method suitable for use by non-experts, which will give good, reliable models without the pitfalls of chance correlations, overfitting, overtraining, poor variable selection etc. We have developed Bayseian neural nets to provide robust SAR mapping, ARD (automatic relevance detection) for variable selection, Gaussian processes for mapping, and a number of new molecular descriptors such as molecular eigenvalues, molecular multipole moments, and new topological indices. I will try to find some current useful textx/reviews for you but also suggest you look at very recent papers by our group, and Yvonne Martin. The Journal of Chemical Information and Computer Science (ACS) is the best place to look for contemporary work in this area. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au 4)my comp chem web page has links to qsar stuff: http://www.dakotacom.net/~bear/compchem.html Soaring Bear Ph.D. Research Pharmacologist, Informatics, Chemistry & Biochemistry, Herbalist & Healthy Lifestyles Herbal Science: http://www.amfoundation.org/herbmed.htm My web tools: http://www.dakotacom.net/~bear email: bear@dakotacom.net, sbear@uswestmail.net fax: 559-663-5833, 520-795-9350 5)The following chapters in "The Encyclopedia of Computational Chemistry" (Paul Schleyer et al. Eds. John Wiley & Sons: Chichester, 1998, ISBN: 0-471-96588-X) covers QSAR: Environmental Chemistry: QSAR Qnatitative Structure-Activity Relationships in Drug Design Qnatitative Structure-Property Relationships (QSPR) Structure-Activity Relationships in Modeling Nucleic Acid Ligand Interactions -Lingran ********************************************************** Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM 6)> You will find the following chapters from Reviews in Computational Chemistry helpful: E. L. Plummer, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 119-168. L. H. Hall and L. B. Kier, RCC, 1991, Vol. 2, pp. 367-422. I. B. Bersuker and A. S. Dimoglo, RCC, 1991, Vol. 2, pp. 423-460. L. M. Balbes, S. W. Mascarella, and D. B. Boyd, RCC, 1994, Vol. 5, pp. 337-379. G. A. Arteca, RCC, 1996, Vol. 9, pp. 191-253. E. J. Martin, D. C. Spellmeyer, R. E. Critchlow Jr., and J. M. Blaney, RCC, 1997, Vol. 10, pp. 75-100. T. I. Oprea and C. L. Waller, RCC, Wiley, 1997, Vol. 11, pp. 127-182. P.-A. Carrupt, B. Testa, and P. Gaillard, RCC, Wiley, 1997, Vol. 11, pp. 241-315. Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu 7): The following few references (and the references cited therein) will provide you with detail descriptions on QSAR (both methods and applications). 1. "Exploring QSAR" Vol 1 and 2, Hansch, C. et al., 1995. ACS publication. 2. "Comprehensive Medicinal Chemistry", Vol 4 (Rational Drug Design), Hansch et. (Des)., 1990, Pergamon Press. 3. "Classical and Three-Dimensional QSAR in Agrochemistry", Hansch, C. and Fujita, T. (Des), 1995, ACS Symposium Series. 4. "Medicinal Chemistry Vol. 19 (Quantitative Structure-Activity Relationships of Drugs)", Topliss, J.G. (ed), 1983, Academic Press. 5. "Quantitative Drug Design. A critical introduction", Martin, Y.C., 1978, Marcel Dekker. 6. "Strategy of Drug Design. A Molecular Guide to Biological Activity" Purcell, W. P., et al. , 1973, Wiley. 7. "3D QSAR in Drug Design, Theory, Methods and Application." Kubinyi, H. (Ed)., 1993, ESCOM Science Publishers. 8. "Perspectives in Drug Discovery and Design, Vols. 9/10/11 (3D QSAR in Drug Design: Ligand-Protein Interactions and Molecular Similarity", Kubinyi, H. et al. (Des), 1998, Kluwer/ESCOM. 9. "Perspectives in Drug Discovery and Design, Vols. 12/13/14 (3D QSAR in Drug Design: Recent Advances", Kubinyi, H. et al. (Des), 1998, Kluwer/ ESCOM. I just wrote a chapter on QSAR in a book and if you are interested I will send you a reprint when the book comes out later this year. Hope this helps. Asim Debnath 8)The following chapters in "The Encyclopedia of Computational Chemistry" (Paul Schleyer et al. Eds. John Wiley & Sons: Chichester, 1998, ISBN: 0-471-96588-X) covers QSAR: Environmental Chemistry: QSAR Qnatitative Structure-Activity Relationships in Drug Design Qnatitative Structure-Property Relationships (QSPR) Structure-Activity Relationships in Modeling Nucleic Acid Ligand Interactions -Lingran ********************************************************** Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM ********************************************************** 9)Allen Richon's article "An Introduction to QSAR Methodology" on the web http://www.netsci.org/Science/Compchem/feature19.html" gives a simple, elegant and meaning of QSAR for starters. It also talks about PLS and crossvalidation too.. Best, Sree *********************************************************** Dr. Sreedhara V Rao Fulmer Synthesis Rm 468 1401 NE Merman Drive, Department of Chemistry Terrace Apt #902 Washington State University Pullman, WA-99163 Pullman, WA 99164-4630. Ph: 509-335-5754/4643 509-334-5980(res) Fx: 509-335-8867 voleti@wsunix.wsu.edu voleti@mail.wsu.edu http://www.wsu.edu/~voleti 10)A source of good information concerning QSAR can be found on the "QSAR & Modelling Society" web-page. They offer lists of books, articles, datasets and much more. Check it out at --> http://www.pharma.ethz.ch/qsar/ regards, Greg +-----------------------------------------------------------+ | Gregory L. Durst computational chemist | | Lilly Research Laboratories tele: 317/433-3386 | | Lilly Corporate Center email: gdurst@lilly.com | | Indianapolis, IN 46285 USA | +-----------------------------------------------------------+ 11)You might want to consider the following references. They probably will not be the complete answer for you but they should help: 1. Ajay, Murcko, M. A. 1995. Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes. J. Med. Chem. 38:4953-67 2. Kansy, M., Ulmschneider, M., van de Waterbeemd, H. 1995. 3D Structural Databases in the Olfactophore Generation of Musk Odor. In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, ed. :633-38. : Prous Science Publishers 3. Livingstone, D. 1995. Data Analysis for Chemists. ISBN Number 0 19 855728 0. Oxford: Oxford University Press 4. Pearlman, R. S., Smith, K. M. 1999. Metric Validation and the Receptor-Relevant Subspace Concept. J. Chem. Inf. Comput. Sci. 39:28-353 5. Rogers, D., Hopfinger, A. J. 1994. Application of Genetic Function Approximation to Quantitative Structure-Activity Relationships and Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 34:854-66 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Senior Scientist, Training Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121 12)Recently I was also looking for a review on QSAR and here is what I got by searching Current Contents from 1993 on. If you find something else, please, let me know. Sincerely, Darko Babic Institute "Rudjer Boskovic" HR-10001 Zagreb, P.O.B. 1016 Croatia ------------------------------------------------------------------------- <1> Authors Kubinyi H. Title QSAR AND 3D QSAR IN DRUG DESIGN .2. APPLICATIONS AND PROBLEMS [Review] Source Drug Discovery Today. 2(12):538-546, 1997 Dec. Local Messages IRB Abstract QSAR already plays an important role in lead structure optimization and it can be predicted that QSAR methods will become essential for handling the huge amount of data associated with combinatorial chemistry. 3D QSAR has already been successfully applied to many data sets of enzyme and receptor ligands. The theory and methodology of these approaches were outlined in Part 1 of this article, published in the November issue. In the second part of this two-part review, the author explains the applications of these methods and addresses the associated problems. [References: 43] <2> Authors Kubinyi H. Title QSAR AND 3D QSAR IN DRUG DESIGN .1. METHODOLOGY [Review] Source Drug Discovery Today. 2(11):457-467, 1997 Nov. Local Messages IRB Abstract Classical QSAR methods describe structure-activity relationships in terms of physicochemical parameters and steric properties (Hansch analysis, extrathermodynamic approach), or certain structural features (Free Wilson analysis). 3D QSAR methods, especially comparative molecular field analysis, consider the three-dimensional structures and the binding modes of protein ligands. Quantitative similarity-activity relationships derive correlations between the similarities of individual compounds and their biological activities. Theory and methodology of these approaches are described here, together with the proper use of regression and partial least squares analyses for deriving quantitative structure-activity relationships. Part 2, to be published in the December issue, will address applications and problems. [References: 45] <3> Authors Fujita T. Title RECENT SUCCESS STORIES LEADING TO COMMERCIALIZABLE BIOACTIVE COMPOUNDS WITH THE AID OF TRADITIONAL QSAR PROCEDURES [Review] Source Quantitative Structure-Activity Relationships. 16(2):107-112, 1997 Apr. Local Messages IRB Abstract New successful applications of the Hansch-type traditional QSAR to key steps in designing novel bioactive compounds are reviewed. Studies for a benzhydrylbenzylpiperazine antimigraine agent (lomerizine), azole-type agricultural fungicides (metconazole and ipconazole), and a biphenylyloxobutanoic acid antiinflammatory agent (flobufen) were taken as the examples. Structural optimizations were nicely made by using the QSAR information sometimes along with findings obtained from 3D molecular modelling studies and/or hypotheses proposed for metabolic fates. The two azole fungicides were launched in 1994. The antimigraine and antiinflammatory agents are expected to be commercialized soon. [References: 27] <4> Authors Maddalena DJ. Title APPLICATIONS OF ARTIFICIAL NEURAL NETWORKS TO QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS [Review] Source Expert Opinion on Therapeutic Patents. 6(3):239-251, 1996 Mar. Local Messages IRB Abstract This review article examines the role of supervised and unsupervised artificial neural networks (ANNs) in the field of quantitative structure-activity relationships (QSAR). They were found to be useful in both classical QSAR and structure-property correlation (SPC) studies where the data sets contain significant non-linear relationships. New applications of ANNs, including methods of descriptor optimisation, simultaneous prediction of multiple descriptors, the development of flexible pharmacophore models and new methods for the multidimensional reduction and display of data sets suggest that ANNs will have a useful role in the field of QSAR in the future. [References: 61] <5> Authors Karelson M. Lobanov VS. Katritzky AR. Title QUANTUM-CHEMICAL DESCRIPTORS IN QSAR/QSPR STUDIES [Review] Source Chemical Reviews. 96(3):1027-1043, 1996 May. Local Messages IRB <6> Authors Hansch C. Hoekman D. Gao H. Title COMPARATIVE QSAR - TOWARD A DEEPER UNDERSTANDING OF CHEMICOBIOLOGICAL INTERACTIONS [Review] Source Chemical Reviews. 96(3):1045-1075, 1996 May. Local Messages IRB <7> Authors Kaminski JJ. Title COMPUTER-ASSISTED DRUG DESIGN AND SELECTION [Review] Source Advanced Drug Delivery Reviews. 14(2-3):331-337, 1994 Jun-Jul. Local Messages IRB Abstract Comparative molecular field analysis (CoMFA), a promising new statistical and graphic three-dimensional quantitative structure-activity relationship (3D-QSAR) technique, and its potential in the drug discovery and design process are reviewed. CoMFA, a computer-assisted 3D-QSAR analysis tool, attempts to correlate molecular shape descriptors defined for a set of substrate (drug) molecules with their observed biological activities. The molecular shape descriptors for each substrate (drug) molecule are determined by analysis of the steric and electrostatic fields that surround a molecule using a test probe atom. CoMFA can also be used to predict the biological activity of unknown substrates in a series of compounds. [References: 20] <8> Authors Stone M. Jonathan P. Title STATISTICAL THINKING AND TECHNIQUE FOR QSAR AND RELATED STUDIES .2. SPECIFIC METHODS [Review] Source Journal of Chemometrics. 8(1):1-20, 1994 Jan-Feb. Local Messages IRB Abstract Twenty-two contrasting statistical methods are reviewed for their applicability to QSAR studies and similar prediction-oriented fields. Each method is concisely specified prior to explanatory or critical comment. [References: 40] <9> Authors Stone M. Jonathan P. Title STATISTICAL THINKING AND TECHNIQUE FOR QSAR AND RELATED STUDIES .1. GENERAL THEORY [Review] Source Journal of Chemometrics. 7(6):455-475, 1993 Nov-Dec. Local Messages IRB Abstract The two parts of this paper form a critique of a variety of statistical techniques of actual or potential use in quantitative structure-activity relationship (QSAR) studies and related fields. Part I explores the statistical thinking that is needed to underpin those techniques. Emphasis is placed on (a) the role of 'exchangeability' as an alternative to unrealistic statistical modelling and (b) the use of cross-validation to limit self-deception in the use of any particular technique. The problem of the almost unlimited range of molecular descriptors is seriously addressed. (Part II provides a concise critical review of methods - some well-established and some new.) [References: 71] <10> Authors Domine D. Devillers J. Chastrette M. Karcher W. Title NON-LINEAR MAPPING FOR STRUCTURE ACTIVITY AND STRUCTURE PROPERTY MODELLING [Review] Source Journal of Chemometrics. 7(4):227-242, 1993 Jul-Aug. Local Messages IRB Abstract From a review of the theoretical aspects of non-linear mapping and the different algorithms available in the literature, the methodological and practical problems linked to the use of this multivariate method in structure-activity and structure-property relationship studies are underlined. Useful tools for the graphical display of the outputs and the interpretation of the obtained clusters are presented. Statistical parameters estimating the quality of the graphical representation of each individual are also introduced. An example of application on a data matrix of 37 acaricides described by four physicochemical descriptors (pi, F, R, MR) is presented. [References: 81] Roberta G. Susnow Physiome Sciences Scientist TEL:609-987-1199 x243 FAX:609-987-9393 307 College Road East Princeton New Jersey 08540 rsusnow@physiome.com From chemistry-request@server.ccl.net Thu Feb 3 13:46:48 2000 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA04435 for ; Thu, 3 Feb 2000 13:46:47 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id MAA01200; Thu, 3 Feb 2000 12:43:30 -0500 (EST) Date: Thu, 3 Feb 2000 12:43:29 -0500 (EST) From: Iraj Daizadeh To: chemistry@ccl.net, pdb-l@rcsb.org Subject: Identifying water in proteins In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII --- Are there any programs that identify water molecules within a protein (from crystallographic data)? We have a one paper which referenced the GRIN/GRID program from Molecular Discovery Ltd., UK....any information would on this or other programs would be appreciated.... Will summarize as typical....iraj Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh From chemistry-request@server.ccl.net Thu Feb 3 15:11:06 2000 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04834 for ; Thu, 3 Feb 2000 15:11:06 -0500 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP); Thu, 3 Feb 2000 19:05:20 +0000 Message-ID: <000d01bf6e7a$4d313840$072c2880@ucl.ac.uk> Reply-To: "Artem R. Oganov" From: "Artem R. Oganov" To: chemistry Subject: CCL: postscript to pcx Date: Thu, 3 Feb 2000 19:10:14 -0000 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 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear CCL'ers, Which programs can you recommend me for converting postscript (*.ps) files into *.pcx, *.bmp, *.jpeg or *.gif format. I will summarise on request. Thanks a lot. ************************************************** Artem R. Oganov, Crystallography and Mineral Physics, Dept. of Geological Sciences, University College London, Gower Street, London WC1E 6BT, U.K. E-mail : a.oganov@ucl.ac.uk Tel. : +44 (020)-7679-3449 Fax : +44 (020)-7679-1612 http://slamdunk.geol.ucl.ac.uk/~artem ************************************************** From chemistry-request@server.ccl.net Thu Feb 3 15:33:49 2000 Received: from netra.ksu.edu.sa ([212.138.39.67]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04994 for ; Thu, 3 Feb 2000 15:33:47 -0500 Received: from sun1.ksu.edu.sa (sun1.ksu.edu.sa [212.138.39.3]) by netra.ksu.edu.sa (8.9.0/8.9.0) with ESMTP id WAA18822 for ; Thu, 3 Feb 2000 22:30:37 -0300 (Etc/GMT) Received: from localhost (azhary@localhost) by sun1.ksu.edu.sa (8.9.0/8.7.3) with SMTP id WAA16918 for ; Thu, 3 Feb 2000 22:29:04 -0300 (GMT) Date: Thu, 3 Feb 2000 22:29:04 -0300 (GMT) From: "Adel Abbas Ali Elazhary Sci. College" X-Sender: azhary@sun1 To: chemistry@ccl.net Subject: basis set for metal complexes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ccl members" I am doing DFT calculations on metal complexes with organic molecules and do not know what basis set should I use. Is there any study about basis set effect on DFT calculated geometry or ir spectrum of metal complexes. It might even help if someone suggest a test molecule for which its vibrational spectrum (especially the bands corresponding to the metal vibrations) are known. Thanking you in advance. Best regards, Adel El-Azhary From chemistry-request@server.ccl.net Thu Feb 3 16:10:37 2000 Received: from ntsvexch.albmolecular.com (mail.albmolecular.com [205.247.153.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA05199 for ; Thu, 3 Feb 2000 16:10:35 -0500 Received: by Ntsvexch with Internet Mail Service (5.5.2650.21) id <1D2CQTTB>; Thu, 3 Feb 2000 15:06:49 -0500 Message-ID: <80F79FF3ECD6D1119D9000805FCC602A82CCA4@Ntsvexch> From: "Andruski, Stephen W." To: "'CCL'" Subject: Re postscript to pcx Date: Thu, 3 Feb 2000 15:06:43 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain Artem R. Oganov wrote: >>Which programs can you recommend me for converting postscript >>(*.ps) files into *.pcx, *.bmp, *.jpeg or *.gif format. I will summarise >>on request. Thanks a lot. The program GhostScript will do this by "printing" to a "pcx", "bmp" or "jpeg" device. GhostScript and GhostView are available for a number of platforms. Information is available at: http://www.cs.wisc.edu/~ghost/aladdin/ Steve Andruski > *********************************** > Dr. Stephen W. Andruski > Senior Research Chemist II > Albany Molecular Research, Inc. > 21 Corporate Circle > Albany, New York 12203 USA > Tel. (518) 464-0279, Ext. 2414 > Fax (518) 464-0289 > E-mail: stephena@albmolecular.com > http://www.albmolecular.com > ************************************ > > > > From chemistry-request@server.ccl.net Thu Feb 3 15:14:45 2000 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04878 for ; Thu, 3 Feb 2000 15:14:44 -0500 Received: from qtp.ufl.edu (ntcrim3 [128.227.192.137]) by qtp.ufl.edu (8.9.1a/8.9.1) with ESMTP id OAA01509; Thu, 3 Feb 2000 14:03:24 -0500 (EST) Message-ID: <3899D1D9.E822271D@qtp.ufl.edu> Date: Thu, 03 Feb 2000 14:07:05 -0500 From: Judy Parker Organization: Quantum Theory Project To: chemistry@ccl.net Subject: Mike Zerner's memorial service Dear Friends, Yesterday we wrote to tell you of the sad news that Mike Zerner died. Some arrangements have now been made that we want to make you aware of. There will be a memorial service for Mike in University Auditorium at the University of Florida on Monday, February 7, at 2:00 in the afternoon. Mike will be buried in Hull, Massachusetts, the town where he was born. In lieu of flowers, Anna and the family have requested that memorials be in the form of contributions to the Michael C. Zerner Memorial Fund. Checks should be made payable to the University of Florida Foundation (Zerner Memorial Fund), and sent to Ms. Jill Rench University of Florida Department of Chemistry P.O. Box 117200 Gainesville, Florida 32611-7200. Mike's friends and colleagues at QTP fn:Judy Parker fax:352-392-8722 work:Phone: 352-846-1125 url:http://www.qtp.ufl.edu/~parker/ University of Florida;Quantum Theory Project email:parker@qtp.ufl.edu title:Office Manager 2308 New Physics Building #92 P.O. Box 118435 Gainesville;FL;32611-8435 From chemistry-request@server.ccl.net Thu Feb 3 17:23:52 2000 Received: from rock.helsinki.fi (rock.helsinki.fi [128.214.3.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05637 for ; Thu, 3 Feb 2000 17:23:51 -0500 Received: from localhost (sundius@localhost) by rock.helsinki.fi (8.9.3/8.9.3) with ESMTP id XAA28411; Thu, 3 Feb 2000 23:18:23 +0200 (EET) Date: Thu, 3 Feb 2000 23:18:22 +0200 (EET) From: Tom Sundius X-Sender: sundius@rock.helsinki.fi To: Christoph.van.Wuellen@ruhr-uni-bochum.de cc: chemistry@ccl.net Subject: Re: CCL:Re, References on exact solutions ... In-Reply-To: <20000203084932.5326.qmail@sgi249.rz.ruhr-uni-bochum.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 3 Feb 100 Christoph.van.Wuellen@ruhr-uni-bochum.de wrote: > I wonder if during this discussion is has been pointed out that H2+ is > a three-body system. The "exact" solution discussed so far is however the > solution of a one-body Schroedinger equation with the clamped nuclei > hamiltonian. Of course there is no analytical solution to a three-body problem. But a complete numerical solution by separation of the variables was already given in 1927 by Oyvind Burrau in Denmark. His solution to the problem in the book by Pauling and Wilson (Introduction to Quantum Mechanics, sect. 42c). This solution was later improved by Hylleraas and Jaffe. The results were in very close agreement with experiment. Tom Sundius University of Helsinki, Department of Physics phone +358-9-191 8339 P.O.Box 9, FIN-00014 Helsinki, Finland fax +358-9-191 8680 From chemistry-request@server.ccl.net Thu Feb 3 17:01:33 2000 Received: from smtp6.mindspring.com (smtp6.mindspring.com [207.69.200.110]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA05551 for ; Thu, 3 Feb 2000 17:01:33 -0500 Received: from piilibrary.ameritech.net (user-33qtdd2.dialup.mindspring.com [199.174.181.162]) by smtp6.mindspring.com (8.9.3/8.8.5) with SMTP id PAA30754 for ; Thu, 3 Feb 2000 15:56:02 -0500 (EST) Message-ID: <001201bf6e89$171525a0$a2b5aec7@ameritech.net> Reply-To: "Jim Kress" From: "Jim Kress" To: "chemistry" References: <000d01bf6e7a$4d313840$072c2880@ucl.ac.uk> Subject: Re: CCL:postscript to pcx Date: Thu, 3 Feb 2000 15:55:59 -0500 Paintshop Pro (www.jasc.com) is an excellent program for doing these types of conversions as well a doing most other graphic image creation/ manipulation/ ... Jim > Dear CCL'ers, > > Which programs can you recommend me for converting postscript > (*.ps) files into *.pcx, *.bmp, *.jpeg or *.gif format. I will summarise > on request. Thanks a lot. >