From parthi@aero.iisc.ernet.in Thu Feb 13 00:22:49 1997 Received: from naveen.ncst.ernet.in for parthi@aero.iisc.ernet.in by www.ccl.net (8.8.3/950822.1) id AAA02033; Thu, 13 Feb 1997 00:10:48 -0500 (EST) Received: from iisc.ernet.in (iisc.ernet.in [144.16.64.3]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with ESMTP id JAA10544 for ; Thu, 13 Feb 1997 09:57:08 +0530 Received: from aero.iisc.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-8.6.5) id JAA09435; Thu, 13 Feb 1997 09:51:38 +0530 Received: by aero.iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA21467; Thu, 13 Feb 1997 09:48:51 -0500 Date: Thu, 13 Feb 1997 09:48:50 -0500 (GMT) From: S Parthiban To: chemistry@www.ccl.net Subject: Volume Visualization/BOB Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I am looking for some general information on volume visualization and the packages available for the same (not the commercial packages). Further, I would like to download the Brick of Bytes (BOB) package. I would appreciate to receive the ftp site... from where i can download the BOB. Any help is appreciated. Thanx Parthi From isi@chem.ubbcluj.ro Thu Feb 13 06:22:50 1997 Received: from zeus.ubbcluj.ro for isi@chem.ubbcluj.ro by www.ccl.net (8.8.3/950822.1) id FAA03859; Thu, 13 Feb 1997 05:41:35 -0500 (EST) Received: from chem.ubbcluj.ro (isi@chem.ubbcluj.ro [193.226.40.193]) by zeus.ubbcluj.ro (8.7.5/8.7.3) with ESMTP id MAA07326 for ; Thu, 13 Feb 1997 12:42:39 +0200 Received: (from isi@localhost) by chem.ubbcluj.ro (8.6.12/8.6.9) id MAA20564; Thu, 13 Feb 1997 12:42:30 +0200 Date: Thu, 13 Feb 1997 12:42:27 +0200 (GMT+0200) From: Ioan SILAGHI-DUMITRESCU To: chemistry@www.ccl.net Subject: solvent effect, vibrational spectra Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody! I am interested in modeling the effect of solvents on the position and shape of vibrational bands of some dithiophosphorus compounds. Could somebody direct me to a PC software which handle such problems? Thank you for your time. Ioan Silaghi-D dr. Ioan Silaghi-Dumitrescu Department of Chemistry Babes-Bolyai University R-3400 Cluj-Napoca, Romania e-mail: isi@chem.ubbcluj.ro fax: +40-64-190818 telephone: +40-64-193833 ext.16 From Gerald.Loeffler@univie.ac.at Thu Feb 13 07:22:58 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id HAA04339; Thu, 13 Feb 1997 07:10:24 -0500 (EST) Received: from indigo (indigo.imp.univie.ac.at [131.130.80.4]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id NAA12660; Thu, 13 Feb 1997 13:09:32 +0100 Sender: gerald@mailbox.univie.ac.at Message-ID: <330382F7.ABD@univie.ac.at> Date: Thu, 13 Feb 1997 13:09:11 -0800 From: Gerald Loeffler Organization: I.M.P. X-Mailer: Mozilla 3.01 (X11; I; IRIX 6.2 IP20) MIME-Version: 1.0 To: Computational Chemistry List CC: Gerald Loeffler Subject: Approximate Water Treatment in MD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Compuational Chemists! Question: Which kind of approximate treatment of water in MD-simulations of solvated systems have you used or do you know of? Background: The inclusion of many explicit water molecules in the MD-simulation of solvated systems guarantees the most detailed description of hydration effects, and is the most natural way of simulating a solution. However, this method is notoriously wasteful in terms of CPU-time, if one is not interested in the water itself but only in the effect of the water on the solute molecule. In an attempt to account for solvation effects in a computationally cheaper way, approximate descriptions of water have been developed. Usually, these water models are based on some sort of continuum model of water. My question is, what computationally cheap treatments of water have people actually tested in MD-simulations, and how did these water models perform? Thank you very much in advance, gerald -- Gerald Loeffler PostDoc in Theoretical Biochemistry EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From s.hogg@ic.ac.uk Thu Feb 13 08:22:53 1997 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA04473; Thu, 13 Feb 1997 07:24:06 -0500 (EST) From: Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 0.57 #1) id 0vv0Cp-0001WA-00; Thu, 13 Feb 1997 12:24:03 +0000 Received: from mtcmsa.mt.ic.ac.uk (mtcmsag1.mt.ic.ac.uk [155.198.96.22]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id MAA22172 for ; Thu, 13 Feb 1997 12:23:47 GMT Received: from mtcsh.mt.ic.ac.uk by mtcmsa.mt.ic.ac.uk (5.x/4.1) id AA00034; Thu, 13 Feb 1997 12:23:46 GMT Message-Id: <15511.9702131223@mtcsh.mt.ic.ac.uk> Subject: MM2 for Linux and/or Win95 ?? To: chemistry@www.ccl.net Date: Thu, 13 Feb 1997 12:23:45 +0000 (GMT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Can anyone give me any pointers to Molecular Mechanics packages that are freeware and run on either Win95 or Linux?? Accuracy and complexity are not an issue - I just want to be able to do some minimisations on fairly small molecules. Time (speed) (within reason) is also not an issue. Any pointers ?? -- Simon Hogg Imperial College, London, UK owner of glass-list@ic.ac.uk From nieder@rs3.thch.uni-bonn.de Thu Feb 13 10:22:53 1997 Received: from IBM.rhrz.uni-bonn.de for nieder@rs3.thch.uni-bonn.de by www.ccl.net (8.8.3/950822.1) id KAA05643; Thu, 13 Feb 1997 10:08:27 -0500 (EST) Received: from rs3.thch.uni-bonn.de by IBM.rhrz.uni-bonn.de (IBM VM SMTP V2R2) with TCP; Thu, 13 Feb 97 16:07:18 MEZ Received: by rs3.thch.uni-bonn.de (AIX 3.2/UCB 5.64/4.03) id AA23759; Thu, 13 Feb 1997 16:06:11 +0100 From: nieder@rs3.thch.uni-bonn.de (Christoph Niederalt) Message-Id: <9702131506.AA23759@rs3.thch.uni-bonn.de> Subject: gaussian94 question To: chemistry@www.ccl.net Date: Thu, 13 Feb 97 16:06:11 MEZ X-Mailer: ELM [version 2.3 PL2] Dear Netters, Is there any possibility to calculate *transition* quadrupol moments with Gaussian94 (beside quadrupol moments for states)? Thank you very much for any help, I will summarize the answers. Christoph Niederalt nieder@rs3.thch.uni-bonn.de From robert@europa.chem.uga.edu Thu Feb 13 10:35:15 1997 Received: from europa.chem.uga.edu for robert@europa.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id JAA05427; Thu, 13 Feb 1997 09:47:17 -0500 (EST) Received: from europa (robert@localhost [127.0.0.1]) by europa.chem.uga.edu (8.6.12/8.6.9) with SMTP id JAA08926; Thu, 13 Feb 1997 09:48:29 -0500 Sender: robert@europa.chem.uga.edu Message-ID: <330329BC.75EC1DB0@europa.chem.uga.edu> Date: Thu, 13 Feb 1997 09:48:28 -0500 From: Jenn-Huei Lii Organization: Computational Center for Molecular Structure and Design (CCMSD) X-Mailer: Mozilla 2.0 (X11; I; Linux 1.3.15 i586) MIME-Version: 1.0 To: s.hogg@ic.ac.uk CC: chemistry@www.ccl.net Subject: Re: CCL:MM2 for Linux and/or Win95 ?? References: <15511.9702131223@mtcsh.mt.ic.ac.uk> Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit Hi Simmon, MM3(96) will run on Linux. It is available to academic users from QCPE. Unfortunatly, it is not free. -Robert s.hogg@ic.ac.uk wrote: > > Can anyone give me any pointers to Molecular Mechanics packages that are > freeware and run on either Win95 or Linux?? > > Accuracy and complexity are not an issue - I just want to be able to do some > minimisations on fairly small molecules. Time (speed) (within reason) is > also not an issue. > > Any pointers ?? > > -- Simon Hogg > Imperial College, London, UK > owner of glass-list@ic.ac.uk > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: s.hogg@ic.ac.uk > -- Original Sender From: Address: s.hogg@ic.ac.uk > 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 ponder@dasher.wustl.edu Thu Feb 13 10:42:39 1997 Received: from dasher.wustl.edu for ponder@dasher.wustl.edu by www.ccl.net (8.8.3/950822.1) id KAA05699; Thu, 13 Feb 1997 10:20:08 -0500 (EST) From: Received: from localhost by dasher.wustl.edu (5.65v3.2/1.1.10.5/12Feb97-1108AM) id AA07021; Thu, 13 Feb 1997 09:20:30 -0600 Message-Id: <9702131520.AA07021@dasher.wustl.edu> To: CHEMISTRY@www.ccl.net Cc: ponder@dasher.wustl.edu Subject: Re: CCL:MM2 for Linux and/or Win95 ?? In-Reply-To: Your message of "Thu, 13 Feb 97 12:23:45 GMT." <15511.9702131223@mtcsh.mt.ic.ac.uk> Date: Thu, 13 Feb 97 09:20:30 -0600 X-Mts: smtp >> >> SIMON HOAG writes: >> > Can anyone give me any pointers to Molecular Mechanics packages that are > freeware and run on either Win95 or Linux?? > Accuracy and complexity are not an issue - I just want to be able to do some > minimisations on fairly small molecules. Time (speed) (within reason) is > also not an issue. > Any pointers ?? > -- Simon Hogg > Imperial College, London, UK > owner of glass-list@ic.ac.uk Please try our TINKER molecular mechanics/dynamics package. It implements several different force fields (MM2/3, AMBER, CHARMM-22, AMBER/OPLS, etc.), and comes with complete source code and scripts to build it on essentially any Unix, and on Win95 using either the MS Powerstation Fortran or the Watcom Fortran compilers. The home page for the package can be found on the Web at http://dasher.wustl.edu. We just got access to a Linux machine and should have an "official" version for Linux soon. In the meantime, if executation speed is not an issue, we know that f2c-->gcc--> executables work (slowly) on every machine we've tried so far. -------- 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 boufer@cennas.nhmfl.gov Thu Feb 13 11:22:54 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id LAA06300; Thu, 13 Feb 1997 11:22:41 -0500 (EST) Received: (from boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) id LAA17945 for chemistry@www.ccl.net; Thu, 13 Feb 1997 11:22:30 -0500 (EST) From: Ahmed Bouferguene Message-Id: <199702131622.LAA17945@cennas.nhmfl.gov> Subject: SCF FOLLOWING SZABO AND OSTLUND To: chemistry@www.ccl.net Date: Thu, 13 Feb 1997 11:22:30 -0500 (EST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear netters, I am trying to write a simple SCF procedure following the quantum chemistry text of Szabo and Ostlund. Actually, I am using the canonical orthogonalization. Howver, after diagonalization process, the eigenvalues and eigenvectors are different(completely) according to whether some eigenvectors of the overlap matrix were dropped or not. According to Szabo and Ostlund, numerical instabilities will occur for overlap eigenvalues smaller than 1.E-4. I would appreciate receiving any comments about this and may be a good reference on this topic. Thanks in advance. From 6031SCHRADER@vms.csd.mu.edu Thu Feb 13 11:33:19 1997 Received: from VMSD.CSD.MU.EDU for 6031SCHRADER@vms.csd.mu.edu by www.ccl.net (8.8.3/950822.1) id LAA06269; Thu, 13 Feb 1997 11:18:54 -0500 (EST) Received: from vms.csd.mu.edu by vms.csd.mu.edu (PMDF V5.0-7 #14229) id <01IFD3T140C08X02Q6@vms.csd.mu.edu> for chemistry@www.ccl.net; Thu, 13 Feb 1997 10:18:31 -0600 (CST) Date: Thu, 13 Feb 1997 10:18:31 -0600 (CST) From: "David M. Schrader" <6031SCHRADER@vms.csd.mu.edu> Subject: Great opportunity ... To: chemistry@www.ccl.net Message-id: <01IFD3T15M7M8X02Q6@vms.csd.mu.edu> X-VMS-To: IN%"chemistry@www.ccl.net" X-VMS-Cc: 6031SCHRADER MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT ... for someone looking for an interesting PhD program (fully grant-funded). Give me an e-jingle at 6031schrader@vms.csd.mu.edu. =============================================================================== David M. Schrader Research Professor Department of Chemistry | Telephone numbers: Marquette University | (414) 288-3332 (office) P.O. Box 1881 | (414) 288-7066 (FAX) Milwaukee, WI 53201-1881, USA | (414) 288-3515 (secretary) Internet: 6031schrader@vms.csd.mu.edu =============================================================================== From XIENING@MEENA.CC.UREGINA.CA Thu Feb 13 11:42:44 1997 Received: from veena.cc.uregina.ca for XIENING@MEENA.CC.UREGINA.CA by www.ccl.net (8.8.3/950822.1) id KAA05877; Thu, 13 Feb 1997 10:39:37 -0500 (EST) Received: from meena.cc.uregina.ca by meena.cc.uregina.ca (PMDF V5.1-6 #20153) id <01IFD2K4GTRK9PNQGP@meena.cc.uregina.ca> for chemistry@www.ccl.net; Thu, 13 Feb 1997 09:39:28 CST Date: Thu, 13 Feb 1997 09:39:27 -0600 (CST) From: Ning Xie Subject: hyperchem/Gaussian: why so different In-reply-to: To: hyperchem@hyper.com Cc: chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Hi, there, When I used hyperchem and Gaussian to calculate the bond length and the energy of ZnCl2, I got quite different results. Here is an example: method Zn--Cl bond length(angstrom) Gaussian Hyperchem PM3 0.7234 2.064 AM1 1.2601 2.0674 Anybody know why? Thank you for your responses. ========================================================================= | XIE, NING Tel: (306)585-5262 (O) | | Chemistry Department (306)585-2184 (H) | | University of Regina E-Mail: xiening@meena.cc.uregina.ca | | Regina, SK or: xiening2@max.cc.uregina.ca | | Canada S4S 0A2 | ========================================================================= From bruce@cosy.utmb.edu Thu Feb 13 16:22:57 1997 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.8.3/950822.1) id PAA08502; Thu, 13 Feb 1997 15:24:00 -0500 (EST) Received: by cosy.utmb.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id OAA11529; Thu, 13 Feb 1997 14:24:30 -0600 From: "Bruce A. Luxon" Message-Id: <9702131424.ZM11527@cosy.utmb.edu> Date: Thu, 13 Feb 1997 14:24:22 -0600 Organization: Sealy Center for Structural Biology Reply-To: bruce@nmr.utmb.edu X-Phone: (409) 747-6802 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Helical Axes Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Fellow Netters & Nettees, Does anyone have a routine, a reference or a thought on how to construct the central axis of a DNA or RNA double helix - especially for A-DNA (B is reasonably well-behaved)? I've searched quite a bit and tried several approaches but so far nothing I've dug up is satisfactory for the relatively short segments I'm looking at (e.g. 10-mers or less). Long segments can be done several ways but the short ones are difficult. Hmmm... All info gratefully received. Bruce Luxon -- *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor * * Sealy Center for Structural Biology U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 http://www.hbcg.utmb.edu/ * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From boufer@cennas.nhmfl.gov Thu Feb 13 16:36:37 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id PAA08586; Thu, 13 Feb 1997 15:38:26 -0500 (EST) Received: (from boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) id PAA19370 for chemistry@www.ccl.net; Thu, 13 Feb 1997 15:38:28 -0500 (EST) From: Ahmed Bouferguene Message-Id: <199702132038.PAA19370@cennas.nhmfl.gov> Subject: SCF Following SZABO AND OSTLUND. To: chemistry@www.ccl.net Date: Thu, 13 Feb 1997 15:38:28 -0500 (EST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi netters, Recently, I've sent an e-mail about the SCF procedure. I am giving in the following a simple numerical example. I have the following overlap matrix : 0.10000000000000D+01 0.99989484007995D+00 0.70348115348149D+00 0.69969766642474D+00 0.99989484007995D+00 0.10000000000000D+01 0.69969766642474D+00 0.69602330987765D+00 0.70348115348149D+00 0.69969766642474D+00 0.10000000000000D+01 0.99989484007995D+00 0.69969766642474D+00 0.69602330987765D+00 0.99989484007995D+00 0.10000000000000D+01 Its eigenvalues are : 0.274360D-04 0.155635D-03 0.600468D+00 0.339935D+01 and the eigenvectors are : -.503096D+00 -.499451D+00 -.496885D+00 0.500548D+00 0.496885D+00 0.500548D+00 -.503096D+00 0.499451D+00 0.503096D+00 -.499451D+00 0.496885D+00 0.500548D+00 -.496885D+00 0.500548D+00 0.503096D+00 0.499451D+00 Following Szabo & Ostlund, the first column should not be used in the iterative process since it correponds to a small eigenvalue (Lower than 1.E-4). Thus when solving the equation H C = E S C where H is the matrix -.11277523049429D+01 -.11280949486585D+01 -.97027798826701D+00 -.96980576230702D+00 -.11280949486585D+01 -.11284603267647D+01 -.96980576230702D+00 -.96938059876316D+00 -.97027798826701D+00 -.96980576230702D+00 -.11277523049429D+01 -.11280949486585D+01 -.96980576230702D+00 -.96938059876316D+00 -.11280949486585D+01 -.11284603267647D+01 The results are as follows : Without dropping the vector correponding to the small eigenvalue I have the following energies : -.127209D+01 -.611606D+00 -.217560D+00 0.446120D+00 And by dropping that eigenvector I have : -.127209D+01 -.527195D+00 -.217560D+00 ---------- The first and the third are correct but the secon is not. That's my trouble. Do not hesitate to give me your point of view. Thanks in advance From zerner@qtp.ufl.edu Thu Feb 13 23:22:59 1997 Received: from qtp.ufl.edu for zerner@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id WAA10868; Thu, 13 Feb 1997 22:33:31 -0500 (EST) From: Received: from crunch.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id WAA15707; Thu, 13 Feb 1997 22:14:48 -0500 Received: by crunch.qtp.ufl.edu (SMI-8.6/SMI-SVR4) id WAA15700; Thu, 13 Feb 1997 22:14:47 -0500 Date: Thu, 13 Feb 1997 22:14:47 -0500 Message-Id: <199702140314.WAA15700@crunch.qtp.ufl.edu> To: young@jschem.korea.ac.kr Subject: ZINDO Cc: chemistry@www.ccl.net Thank you for your interest and request for information on ZINDO. We did give out copies of ZINDO until recently free of charge, but the popularity of the program and the very many questions we were receiving on how to run the program, what the results meant, and so forth, exceeded our ability to respond properly and in a timely fashion. As a result we gave ZINDO to MSI (Molecular Simulations, Inc.)to distribute. They have also made a very nice interface for the program, to both ease the preparation of input, and to better visualize the output. They can be reached via rcenter@msi.com or at MSI 9685 Scranton Road San DIego, CA 92121 and the nearest MSI representative will get back to you. This version should contain an SOS for polarizability and hyperpolarizability written originally by Dave Kanis and Bill Parkinson and more lately fixed here by Roscoe Yu and Mike Lee. A latter release will have frequency dependent TDA and RPA including solvent effects, but this is not in the present MSI version. Sincerely, Mike Zerner