From giulio@indigo.farma.unimi.it Mon Jun 1 04:23:18 1998 Received: from indigo.farma.unimi.it (indigo.farma.unimi.it [159.149.11.213]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA20122 Mon, 1 Jun 1998 04:23:13 -0400 (EDT) Received: (from giulio@localhost) by indigo.farma.unimi.it (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA02042 for CHEMISTRY@www.ccl.net; Mon, 1 Jun 1998 10:03:15 -1500 From: "Giulio Vistoli" Message-Id: <9806011003.ZM2040@indigo.farma.unimi.it> Date: Mon, 1 Jun 1998 10:03:15 +0000 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Del Re or Gasteiger atomic charges Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL'ers We are looking for a free software (with C or Fortran source) to calculate the atomic charges with Del Re or Gasteiger approach. Can anybody help us to find a similar program ? Thanks a lot Dr. Giulio Vistoli From jolanala@main.amu.edu.pl Mon Jun 1 09:09:56 1998 Received: from main.amu.edu.pl (main.amu.edu.pl [150.254.65.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA22575 Mon, 1 Jun 1998 09:09:49 -0400 (EDT) From: jolanala@main.amu.edu.pl Received: from ppp (pppa114.poznan.tpnet.pl [194.204.178.114]) by main.amu.edu.pl (8.8.8/8.8.8) with SMTP id OAA05112 for ; Mon, 1 Jun 1998 14:56:26 +0200 (MET DST) Message-Id: <199806011256.OAA05112@main.amu.edu.pl> Comments: Authenticated sender is To: CHEMISTRY@www.ccl.net Date: Mon, 1 Jun 1998 14:52:25 +0002 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: question X-Confirm-Reading-To: jolanala@main.amu.edu.pl X-pmrqc: 1 Return-receipt-to: jolanala@main.amu.edu.pl Priority: normal X-mailer: Pegasus Mail for Win32 (v2.54) Dear all, Does anybody know how many temporary space should be available for Gaussian calculations (ethisterone and other steroids)? Best regards, Jolanta From ijbarani@syr.edu Mon Jun 1 10:17:44 1998 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.1.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA23019 Mon, 1 Jun 1998 10:17:42 -0400 (EDT) Received: from syr.edu (casehead.cat.syr.edu [128.230.59.14]) by mailbox.syr.edu (8.9.0/8.9.0) with ESMTP id KAA04954 for ; Mon, 1 Jun 1998 10:17:44 -0400 (EDT) Message-ID: <3572B7AA.DB4A4E11@syr.edu> Date: Mon, 01 Jun 1998 10:16:10 -0400 From: "Igor J. Barani" Organization: Department of Chemistry at Syracuse University X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: ccl Subject: pdb file manipulator References: <35615AFF.AD658128@chem.hull.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am looking for a pdb file manipulating software (preferably shareware). Simply, I need to manipulate a large pdb file by performing such operations as removing the hydrogens and adding dummy atoms etc. Does anyone know where I can download a shareware program to do just that? Thanks in advance for your responses. Sincerely, Igor Barani -- ________________________________________________ Igor J. Barani, Research Assistant W.M. Keck Center for Molecular Electronics Department of Chemistry at Syracuse University CST 1-014C 111 College Place Syracuse, New York 13244-4100 Email: ijbarani@syr.edu ________________________________________________ From johnw@msi.com Mon Jun 1 11:31:51 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA23491 Mon, 1 Jun 1998 11:31:47 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA25767; Mon, 1 Jun 98 08:17:19 -0700 Received: from mica.msi.com(146.202.6.217) by bioc1.msi.com via smap (V2.0) id xma025763; Mon, 1 Jun 98 08:17:15 -0700 Received: from johnw-pc.msi.com by mica.biosym.com.msi.com (4.1/SMI-4.1) id AA00166; Mon, 1 Jun 98 08:28:09 PDT Received: by localhost with Microsoft MAPI; Mon, 1 Jun 1998 08:21:21 -0700 Message-Id: <01BD8D36.420339E0.johnw@msi.com> From: John Wintersteen Reply-To: "Viewer_Pro (E-mail)" To: "chemistry@www.ccl.net" Subject: CCL:New version of the WebLab Viewer from MSI Date: Mon, 1 Jun 1998 08:21:07 -0700 Organization: Molecular Simulations Inc. X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello, Molecular Simulations is pleased to announce the availability of WebLab ViewerPro 3.1 for Windows 95/NT. This new version of MSI's 3D molecular visualization and communication software includes: - Enhanced clean performance with improved geometry - SMILES file export - Improved query features - Additional display style - Significant enhancements to crystal visualization and building (A 3.1 version of the free WebLab ViewerLite for the PC is also available) We are also please to announce the availability of a beta version the free ViewerLite 3.1 for the Macintosh Power PC. This new version marks a significant improvement in memory usage and performance on the Macintosh. We are actively seeking user input, so after downloading and using this new version, please submit your comments to viewer-support@msi.com. The WebLab Viewer is available from MSI web site at http://www.msi.com/weblab/ We hope that you will enjoy using the new version of the WebLab Viewer, and would be glad to receive your comments. Sincerely, John Wintersteen Product Manager, WebLab Viewer Products Molecular Simulations Inc. http://www.msi.com From tom_halgren@merck.com Mon Jun 1 16:03:53 1998 Received: from mgw2.merck.com (mgw2.merck.com [155.91.4.103]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA26291 Mon, 1 Jun 1998 16:03:51 -0400 (EDT) Message-Id: <199806012003.QAA26291@www.ccl.net> Date: Mon, 01 Jun 1998 16:00:06 -0400 From: "Halgren, Thomas" Subject: Validation suite for MMFF94 now available To: "'Computational Chemistry List'" Cc: "'Donald G. Truhlar'" MIME-version: 1.0 Content-type: text/plain Content-transfer-encoding: 7BIT Dear CCLers, Jan Labanowski has kindly posted on the Computational Chemistry List archives a comprehensive validation suite for MMFF94 that I prepared. The suite contains a README file that defines all other files in the test suite. The most important are: MMFF94_dative.mol2 mol2-format input, using dative bonds for oxysulfur, etc. MMFF94_hypervalent.mol2 mol2 input, using "hypervalent" representations MMFF94.mmd BatchMin/MacroModel dat-format input MMFF94.energies list of BatchMin and Merck-OPTIMOL total energies MMFF94_bmin.log BatchMin output log file MMFF94_opti.log OPTIMOL output file with detailed interaction analyses These input and output files provide data for the test suite, which consists of 753 molecules. There is also a subsidiary file that lists the names of molecules that have alternative dative and hypervalent representations (MMFF94.dative_molecules), and a file that just lists the molecule names and titles (MMFF94.titles). Most of the input data is derived from CSD structures. I wish to thank Steve Salisbury and the Cambridge Crystallographic Data Center for graciously consenting to the use of this data. I also wish to thank Jan Labanowski for his encouragement in the posting of this validation suite and for his role in providing CCL and its archives to the community. My hope is that this data will assist members of the community who have independently implemented MMFF94, or who are in the process of doing so, to validate their efforts (I am aware of four such initiatives, in addition to the BatchMin and CHARMm implementations to which Merck has contributed); it is always difficult to work from published accounts and to be sure you know where you stand. This validation suite should also allow individuals who use an independently developed commercial implementation of MMFF94 to carry out their own validation and to satisfy themselves as to the authenticity of the commercial implementation. Others who are not interested in pursuing MMFF94 per se might view the suite as a source of input data that could be useful in developing and testing other force fields. The MMFF94 validation suite can be accessed at: ftp://www.ccl.net/pub/chemistry/data/MMFF94 or at: http://www.ccl.net/cca/data/MMFF94 I would be pleased to hear of any uses made of this data. Best regards, Tom Halgren voice: 732-594-7735 fax: 732-594-4224 halgren@merck.com From rassolov@chem.nwu.edu Mon Jun 1 17:12:41 1998 Received: from mercury.chem.nwu.edu (root@mercury.chem.nwu.edu [129.105.116.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA26669 Mon, 1 Jun 1998 17:12:41 -0400 (EDT) Received: from b.theory.nwu.edu (b.theory.nwu.edu [129.105.55.21]) by mercury.chem.nwu.edu (8.8.5/8.8.5) with SMTP id QAA22525 for ; Mon, 1 Jun 1998 16:13:12 -0500 (CDT) Received: from localhost by b.theory.nwu.edu (950413.SGI.8.6.12) id QAA08891; Mon, 1 Jun 1998 16:12:41 -0500 Date: Mon, 1 Jun 1998 16:12:41 -0500 (CDT) From: Vitaly Rassolov X-Sender: rassolov@b.theory.nwu.edu Reply-To: Vitaly Rassolov To: chemistry@www.ccl.net Subject: summary: UHF correlation energy Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: A while ago I asked about the availability of atomic correlation energy based on UHF wave functions. Strictly speaking, it is the UHF-based correlation energy which is modeled in traditional DFT theory, so the issue seem to be important. It turns out that nobody had tried to find the UHF corelation energy, as far as CCLers know. One of the possible reasons is that one can estimate the UHF Ecorr. by subtracting the difference (E(rohf)-E(uhf)) from the ROHF-based corr. energy. This difference is rather small and in most cases is comparable to the error in the correlation energy itself. Below is the summary of responses: From: Pablo Vitoria Garcia Dear Vitaly, You may find these references useful: Rosciszewsli,K. "Simple Empirical Formulas and good quality estimatios for electron correlation energies of molecules and molecular clusters: first row atom molecules", International Jourl of Qunatum Chemistry, (1996), 58(5), 471-485 Kristyan, S. "Inmediate estimation of correlation energy for molecular systems from the partial charges on atoms in the molecule", Chem. Phys., (1997), 224(1), 33-51 ***** From: Jaouad El-Bahraoui can you summerized to the CCL please. many thanks ***** Vitaly Rassolov Chemistry Department Northwestern University rassolov@chem.nwu.edu From boyd@chem.iupui.edu Mon Jun 1 17:38:23 1998 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA26889 Mon, 1 Jun 1998 17:38:22 -0400 (EDT) Message-ID: Date: 1 Jun 1998 16:40:03 -0500 From: "Boyd" Return-Receipt-To: "Boyd" Subject: Gordon Conference on Computational Chemistry To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.0.0 CCLers, The deadline for registering for the 1998 Gordon Research Conference on Computational Chemistry is close at hand. A discount of $50 is available to those who register by June 8. For information about the conference, please contact the Chair, Prof. Jeff Madura (madura@mail.cc.duq.edu), or the Vice-Chair, Dr. Terry Stouch (stouch@bms.com). To contact the Gordon Research office, telephone 401-783-4011 or fax 401-783-7644 or email grc@grcmail.grc.uri.edu The dates of the conference are June 28-July 3, 1998, and this year it will be held at Tilton School, Tilton, New Hampshire, for the first time. Further information is on the Web at http://chem.iupui.edu/rcc/grccc.html Jeff and Terry have put together a great meeting. Register quickly. Thanks, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry Editor, Journal of Molecular Graphics and Modelling Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu From john@xray.bmc.uu.se Mon Jun 1 18:15:55 1998 Received: from columba.its.uu.se (columba.its.uu.se [130.238.7.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA27318 Mon, 1 Jun 1998 18:15:53 -0400 (EDT) Received: from alpha2.bmc.uu.se ([130.238.37.65]:4262 "HELO alpha2.bmc.uu.se" ident: "NO-IDENT-SERVICE") by emberiza.its.uu.se with SMTP id <61736-85742>; Tue, 2 Jun 1998 00:15:16 +0200 Received: from janmarel.ANST.UU.SE by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA30110; Tue, 2 Jun 1998 00:14:00 +0200 Date: Tue, 2 Jun 1998 00:17:20 +0200 (MDT) From: John Marelius To: "'Computational Chemistry List'" Subject: mol2 file format description? In-Reply-To: <199806012003.QAA26291@www.ccl.net> Message-Id: X-X-Sender: john@alpha2.bmc.uu.se Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer, if you happen to have a description of the format of mol2 files (used by Sybyl and other software), please e-mail it to me. John Marelius +------------------------------------------------------------------------+ | John Marelius | | Dept. of Molecular Biology, Uppsala University | | E-mail: john@xray.bmc.uu.se | +------------------------------------------------------------------------+