From chemistry-request@server.ccl.net Wed Apr 5 09:24:56 2000 Received: from abacus.ac.BrockU.CA (abacus.ac.BrockU.CA [139.57.65.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA30380 for ; Wed, 5 Apr 2000 09:24:55 -0400 Received: from localhost (srothste@localhost) by abacus.ac.BrockU.CA (8.9.3/8.9.3) with SMTP id JAA363608; Wed, 5 Apr 2000 09:24:16 -0400 (EDT) Date: Wed, 5 Apr 2000 09:24:16 -0400 (EDT) From: "Stuart M. Rothstein" To: sergiusz kwasniewski cc: chemistry@ccl.net Subject: Re: CCL:congresses In-Reply-To: <200004051135.NAA05720@alpha.luc.ac.be> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII dear Sergiusz; I know of no general website on conference announcements. However, there are several symposia of interest to theoretical/computational/polymer chemists at the Pacifichem 2000 congress; Honolulu, 14-19 December 2000. For a list of symposia, some of which have detailed descriptions, consult: http://www.chembio.uoguelph.ca/pac2000/symposia.htm Travel information, etc is given on the conference website: http://www.acs.org/meetings/pacific2000/ The deadline for abstract submission via the web is APRIL 14th. Stuart M. Rothstein, Professor of Chemistry and Physics, Brock University, St. Catharines, Ontario, L2S 3A1 CANADA srothste@abacus.ac.brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/rothstein/ On Wed, 5 Apr 2000, sergiusz kwasniewski wrote: > Hi, > > Does anyone know if there is a website where anouncements for > congresses about theoretical/computational chemistry and/or > polymers available ? > > Thanks, > > S. Kwasniewski > > > ___________________________________________________ > > Sergiusz Kwasniewski > LUC SBG/TS > Universitaire Campus Gebouw D > 3590 Diepenbeek > BELGIUM > > tel(direct): 032 (0)11/268315 > fax : 032 (0)11/268301 > email : sergiusz.kwasniewski@luc.ac.be > http://www.luc.ac.be/Research/TheoChem > ___________________________________________________ > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Apr 6 01:49:18 2000 Received: from mail.anrb.ru ([62.76.11.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA02975 for ; Thu, 6 Apr 2000 01:46:04 -0400 Received: from mail.anrb.ru ([62.76.11.200]) by mail.anrb.ru (8.9.3/8.9.3) with SMTP id LAA16085 for ; Thu, 6 Apr 2000 11:56:31 +0600 Date: Thu, 6 Apr 2000 11:42:10 +0500 From: "Ilfir R. Ramazanov" X-Mailer: The Bat! (v1.036) S/N 0 Reply-To: "Ilfir R. Ramazanov" Organization: Institute of Petrochemistry and Catalysis,Ufa,Russia Priority: Normal Message-ID: <15487.000406@anrb.ru> To: CHEMISTRY@ccl.net Subject: Re: CCL:Refractive Index References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ACD does calculate a refraction index but it has very poor results. And ACD is not a computational chemistry program. Ilfir. amdo> Dear Joe, amdo> Package ACD calculates (Chem Sketch) refraction indexes. amdo> On Wed, 5 Apr 2000, Golab, Joseph T wrote: >> Is it possible to calculate the refractive index of a material using >> computational chemistry techniques either directly or indirectly? >> >> >> :Joe >> golabjt@bp.com >> +1 630 961-7878 (SOCON 231-7878) >> >> >> >> >> >> >> amdo> Andre Mauricio de Oliveira amdo> VOICE +55-031-374-1325 amdo> +55-031-499-5765 amdo> FAX +55-031-499-5700 amdo> Laboratorio de QSAR e Modelagem Molecular amdo> Nucleo de Estudos em Quimica Medicinal (NEQUIM) amdo> NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim amdo> Departamento de Quimica ICEx amdo> Federal University of Minas Gerais amdo> Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 amdo> Belo Horizonte MG Brazil amdo> -= This is automatically added to each message by mailing script =- amdo> CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins amdo> MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH amdo> CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 amdo> Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Best regards, Ilfir R. Ramazanov, Ph.D., Laboratory of Catalytic Synthesis Institute of Petrochemistry and Catalysis, pr. Oktyabrya, 141, Ufa, 450075, Russia. mailto:elf@anrb.ru Visit my homepage and find some QC software http://members.tripod.com/~ChemELF Visit our lab web page http://organomet.cjb.net 06.04.2000 11:37 From chemistry-request@server.ccl.net Thu Apr 6 03:20:06 2000 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA03505 for ; Thu, 6 Apr 2000 03:20:03 -0400 From: quanta@chem.unipune.ernet.in Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id MAA19213 for ; Thu, 6 Apr 2000 12:38:37 +0530 Received: (from quanta@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id NAA06236 for CHEMISTRY@www.ccl.net; Thu, 6 Apr 2000 13:11:08 +0530 Date: Thu, 6 Apr 2000 13:11:08 +0530 Message-Id: <200004060741.NAA06236@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: HYDRATION ?????? April 06, 2000 Can anyone please tell me the fundamental and other related references dealing with hydrophobic hydration and/or hydrophilic hydration. Thanks in advance ANANT From chemistry-request@server.ccl.net Thu Apr 6 04:04:49 2000 Received: from host36.lctn.u-nancy.fr (host36.lctn.u-nancy.fr [192.54.210.43]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA03872 for ; Thu, 6 Apr 2000 04:04:46 -0400 Received: from lctn.u-nancy.fr (localhost [127.0.0.1]) by host36.lctn.u-nancy.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA88134; Thu, 6 Apr 2000 10:08:53 +0200 (MDT) Sender: surjit@lctn.u-nancy.fr Message-ID: <38EC4615.5A2426B2@lctn.u-nancy.fr> Date: Thu, 06 Apr 2000 10:08:53 +0200 From: Surjit Dixit X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: "Stuart M. Rothstein" , chemistry@ccl.net Subject: Re: CCL:congresses References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! The CCL web site itself is a great place to start searching for conferences. http://www.ccl.net the homepage has a link to Announcements and Conferences http://www.ccl.net/chemistry/announcements/conferences/index.shtml Regards, Surjit "Stuart M. Rothstein" wrote: > > dear Sergiusz; > > I know of no general website on conference announcements. However, there > are several symposia of interest to theoretical/computational/polymer > chemists at the Pacifichem 2000 congress; Honolulu, 14-19 December 2000. > > For a list of symposia, some of which have detailed descriptions, consult: > http://www.chembio.uoguelph.ca/pac2000/symposia.htm > Travel information, etc is given on the conference website: > http://www.acs.org/meetings/pacific2000/ > The deadline for abstract submission via the web is APRIL 14th. > > Stuart M. Rothstein, > Professor of Chemistry and Physics, > Brock University, > St. Catharines, Ontario, > L2S 3A1 CANADA > > srothste@abacus.ac.brocku.ca > http://chemiris.labs.brocku.ca/~chemweb/faculty/rothstein/ > > On Wed, 5 Apr 2000, sergiusz kwasniewski wrote: > > > Hi, > > > > Does anyone know if there is a website where anouncements for > > congresses about theoretical/computational chemistry and/or > > polymers available ? > > > > Thanks, > > > > S. Kwasniewski > > > > > > ___________________________________________________ > > > > Sergiusz Kwasniewski > > LUC SBG/TS > > Universitaire Campus Gebouw D > > 3590 Diepenbeek > > BELGIUM > > > > tel(direct): 032 (0)11/268315 > > fax : 032 (0)11/268301 > > email : sergiusz.kwasniewski@luc.ac.be > > http://www.luc.ac.be/Research/TheoChem > > ___________________________________________________ > > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Surjit B. Dixit, Ph.D. Email: surjit@lctn.u-nancy.fr Laboratoire De Chimie Theorique, U.M.R. C.N.R.S. #7565, B.P. 239 University Henry Poincare-Nancy I, 54506 Nancy-Vandoeuvre Cedex, France Phone: 33-3-83.91.20.00 Extn:3588 Fax: 33-3-83.91.25.30 From chemistry-request@server.ccl.net Thu Apr 6 04:04:52 2000 Received: from srvnt01.osmetech.plc.uk (aromascn.demon.co.uk [158.152.95.246]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA03878 for ; Thu, 6 Apr 2000 04:04:51 -0400 Received: by SRVNT01 with Internet Mail Service (5.0.1461.28) id ; Thu, 6 Apr 2000 09:02:18 +0100 Message-ID: <09433A5B7967D3119BE30090278D1123086D4D@SRVNT01> From: Tom Hawkins To: chemistry@ccl.net Subject: RE: congresses Date: Thu, 6 Apr 2000 09:02:17 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1461.28) Content-Type: text/plain; charset="iso-8859-1" There is a searchable database of chemistry conferences at http://www.chemsoc.org Dr Tom Hawkins Osmetech plc Sensor Technologist Electra House, Electra Way, Crewe CW1 6WZ thawkins@osmetech.plc.uk Tel +44(0)1270 216444 Fax +44(0)1270 216030 On Wed, 5 Apr 2000, sergiusz kwasniewski wrote: > Hi, > > Does anyone know if there is a website where anouncements for > congresses about theoretical/computational chemistry and/or > polymers available ? > > Thanks, > > S. Kwasniewski > > > ___________________________________________________ > > Sergiusz Kwasniewski > LUC SBG/TS > Universitaire Campus Gebouw D > 3590 Diepenbeek > BELGIUM > > tel(direct): 032 (0)11/268315 > fax : 032 (0)11/268301 > email : sergiusz.kwasniewski@luc.ac.be > http://www.luc.ac.be/Research/TheoChem > ___________________________________________________ > From chemistry-request@server.ccl.net Thu Apr 6 03:08:26 2000 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA03422 for ; Thu, 6 Apr 2000 03:08:25 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Thu, 6 Apr 2000 09:09:41 +0200 Received: from werkman.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA10694; Thu, 6 Apr 2000 09:08:19 +0200 Date: Thu, 6 Apr 2000 08:03:41 +0200 (CEST) From: David van der Spoel X-Sender: spoel@werkman.bmc.uu.se To: "Ilfir R. Ramazanov" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Refractive Index In-Reply-To: <15487.000406@anrb.ru> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 6 Apr 2000, Ilfir R. Ramazanov wrote: The refractive index can be computed from the frequency dependent dielectric constant, which in turn can be computed from molecular simulation. See my paper (and the 80 references therein): @Article{Spoel98a, author = {D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen}, title = {A systematic study of water models for molecular simulation}, year = 1998, journal = "J. Chem. Phys.", volume = 108, pages = {10220-10230} } an excellent review that covers this is Zhu et al. @Article{Zhu94, author = {S-B. Zhu and S. Singh and G. W. Robinson}, title = {Field-Perturbed Water}, journal = "Adv. Chem. Phys.", year = 1994, volume = 85, pages = {627-731} } Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Thu Apr 6 04:48:41 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA04310 for ; Thu, 6 Apr 2000 04:48:40 -0400 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id KAA19782 for ; Thu, 6 Apr 2000 10:48:31 +0200 (MET DST) Date: Thu, 6 Apr 2000 10:48:31 +0200 (MET DST) Message-Id: <200004060848.KAA19782@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: summary: congresses Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id EAA04311 Hi, I would like to thank all the people who have shared their knowledge about websites where information about congresses / conferences can be found .. The original question was the following: "Does anyone know if there is a website where anouncements for congresses about theoretical/computational chemistry and/or polymers available ?" Here's a short summary: --- 1 --- Pacifichem 2000 congress; Honolulu, 14-19 December 2000. For a list of symposia, some of which have detailed descriptions, consult: http://www.chembio.uoguelph.ca/pac2000/symposia.htm Travel information, etc is given on the conference website: http://www.acs.org/meetings/pacific2000/ The deadline for abstract submission via the web is APRIL 14th. Stuart M. Rothstein, Professor of Chemistry and Physics, Brock University, St. Catharines, Ontario, L2S 3A1 CANADA srothste@abacus.ac.brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/rothstein/ --- 2 --- http://www.ccl.net/chemistry/announcements/conferences/index.shtml Dr. Gloria Ines Cardenas-Jiron Departamento de Quimica de los Materiales, Facultad de Quimica y Biologia, UNIVERSIDAD DE SANTIAGO DE CHILE, Casilla 40 Correo 33, Santiago, CHILE. Fax: (56-2) 681.2108 Phone: (56-2) 681.2575 e-mail: gcardena@lauca.usach.cl --- 3 --- check: http://majestix.msp.univie.ac.at/dates.html and the additional links therein. Andreas Parusel --- 4 --- You can visit http://www.chemcad.fr/news/congres.html. We put all congresses that we receive. It's in French. Cédric Merlot Support Technique ChemCAD 116, rue du Général Gouraud 67210 OBERNAI Tel : 03 88 95 68 52 Fax : 03 88 95 07 92 --- --- Hope this might help .. Serge Kwasniewski ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Thu Apr 6 05:53:30 2000 Received: from lithium.theochem.uni-duesseldorf.de (root@lithium.theochem.uni-duesseldorf.de [134.99.82.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA04808 for ; Thu, 6 Apr 2000 05:53:30 -0400 Received: from borussia.theochem.uni-duesseldorf.de (borussia.theochem.uni-duesseldorf.de [134.99.82.13]) by lithium.theochem.uni-duesseldorf.de (8.8.7/8.8.8) with ESMTP id LAA05874; Thu, 6 Apr 2000 11:49:41 +0200 Received: from [[UNIX: localhost]] ([[UNIX: localhost]]) by borussia.theochem.uni-duesseldorf.de (8.8.7/8.8.8) id LAA00506; Thu, 6 Apr 2000 11:49:42 +0200 From: Wibke Sudholt Reply-To: wibke@theochem.uni-duesseldorf.de To: CHEMISTRY@ccl.net Subject: SUMMARY: Looking for a Code to Solvate Molecules Date: Thu, 6 Apr 2000 10:45:36 +0200 X-Mailer: KMail [version 0.7.9] Content-Type: text/plain Cc: sdecker@LATTE.MEMPHIS.EDU, desingh@syr.edu, Willem_Van_Hoorn@sandwich.pfizer.com, PETERSBK@apci.com, dseverance@acadia-pharm.com, rvenable@deimos.cber.nih.gov, spoel@xray.bmc.uu.se, m.swart@chem.rug.nl MIME-Version: 1.0 Message-Id: <00040611494100.00485@borussia> Content-Transfer-Encoding: 8bit Dear CCLers, two people ask me to present a summary of the responses to my question, so I'll do this with this email (answers are edited a little bit). Most people suggest to use BOSS or a related program, which is a full Monte Carlo package. Since I only need a "small tool", I decided to use the code of Marcel Swart, which seems to fit to my needs very well (hopefully, you don't get too many inquiries now that I sent it to the list, Marcel :-) ). Many thanks to Stephen A. Decker, Deepak Singh for interest; Willem P. van Hoorn, Brian K. Peterson, Daniel Severance, Rick Venable, David van der Spoel, Marcel Swart for providing answers! (in order of appearance in my mailbox; hopefully, I didn't forget anyone) Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de ---------- Original Question ---------- Subject: CCL:Looking for a Code to Solvate Molecules Date: Mon, 3 Apr 2000 14:59:00 +0200 From: Wibke Sudholt Dear CCLers, I am looking for a program (preferably freeware Fortran code) which is capable of the following (or parts of it): * reads in the xyz coordinates of a solute molecule and reads in the xyz coordinates of an (arbitrary, not only water) solvent molecule * generates xyz coordinates of a cubic box filled with the solute molecule surrounded by some kind of random mixture of solvent molecules (needs not to be equilibrated or may have some order left) * controles the size of the system by density, box size, number of solvent molecules etc. I have checked the internet with no success, as most of such programs can only handle water or need predefined boxes filled with solvent molecules (programs which generate those would also be a help). Is anybody out there aware of such a program and willing to share his/her code/knowledge with me? Thank you very much in advance for your help Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de ---------- Answer Message 1 ---------- Subject: RE: Looking for a Code to Solvate Molecules Date: Mon, 3 Apr 2000 15:42:08 +0100 From: Willem_Van_Hoorn@sandwich.pfizer.com BOSS by WL Jorgensen can do (almost all of) what you want, is written in F77, and is academic software: http://zarbi.chem.yale.edu ---------------------------------------------------------------------------- Dr. Willem P van Hoorn IPC 557 Computational Chemistry Phone: +44-1304-648470 Pfizer Central Research Fax : +44-1304-658422 Sandwich Willem_van_Hoorn@sandwich.pfizer.com Kent CT13 9NJ United Kingdom ---------------------------------------------------------------------------- ---------- Answer Message 2 ---------- Subject: RE: Looking for a Code to Solvate Molecules Date: Mon, 3 Apr 2000 10:59:00 -0400 From: "PETERSON,BRIAN K." Hi Wibke. While you may find a solvation code, you might want to look at grand-canonical Monte Carlo codes. While there are some efficiency problems with high density GCMC, for just preparing reasonably equilibrated systems for input into something else, they should work fine. I use the Cerius2 sorption module for this. One GCMC code available on the web is from Thanos Panagiotopoulos' group at: http://thera.umd.edu/jerring/gcmc/overview/overview.htm . brian peterson Air Products and Chemicals, Inc. ---------- Answer Message 3 ---------- Subject: RE: Looking for a Code to Solvate Molecules Date: Mon, 3 Apr 2000 09:33:18 -0700 From: Daniel Severance Hi, The BOSS program from Bill Jorgensen at Yale does just what you want. You can specify your own solvents, and can do 2-part mixtures at least. You do have control over the box size as well. It's not freeware, but he doesn't charge much for academic institutions. He can answer more specifically, since I've never used the solvent mixture options and thus haven't paid attention to any more recent changes he may have made. His e-mail address is bill@adrik.chem.yale.edu Good luck! Dan ---------- Answer Message 4 ---------- Subject: Re: CCL:Looking for a Code to Solvate Molecules Date: Mon, 3 Apr 2000 13:38:57 -0400 (EDT) From: Rick Venable I have some CHARMM scripts I've developed for solvating within any orthorhombic shape (square corners), which I can provide if you are interested in them. I've also recently developed generalized scripts for adding ions to the resulting box, by replacing selected water molecules. Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) ---------- Answer Message 5 ---------- Subject: solvate Date: Tue, 4 Apr 2000 00:11:56 +0200 (CEST) From: David van der Spoel Such a program "genbox" comes with the GROMACS set: http://md.chem.rug.nl/~gmx (and probably with many other MD packages). genbox supports rectangular and triclinic boxes (which basically means all periodic boxes) as well as nonperiodic systems (solvent layer). The type of solvent is determined by your input file, and can be any organic molecule, or mixture thereof. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ---------- Answer Message 6 ---------- Subject: Re: CCL:Looking for a Code to Solvate Molecules Date: Tue, 4 Apr 2000 12:01:42 +0200 From: Marcel Swart Hi Wibke, I've written a program which does just what you want: given a solvent molecule and a solute molecule, you have several options to fill several boxes at random with any given number of solvents/solutes. It is not on the Web yet, cuz I feel I have to improve a bit upon it, incl. Online manual etc., but I'd be happy to give you the source code. If you want, I can make a tar-file of the source code as it is now, and send this to you. Marcel. -- ------------------------------------------------ drs. Marcel Swart Theoretical Chemistry (MSC) Molecular Dynamics (GBB) Rijksuniversiteit Groningen Chemistry Department Nijenborgh 4 9747 AG Groningen The Netherlands tel : +31 - (0)50 - 3634377 fax : +31 - (0)50 - 3634441 E-mail : m.swart@chem.rug.nl WWW: http://theochem.chem.rug.nl/~marcel/ ------------------------------------------------ From chemistry-request@server.ccl.net Thu Apr 6 07:29:52 2000 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06294 for ; Thu, 6 Apr 2000 07:29:45 -0400 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [10.0.0.3]) by mailgw.barc.ernet.in (8.9.1/8.9.1) with ESMTP id SAA04064; Thu, 6 Apr 2000 18:11:08 +0530 Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with SMTP id QAA04303; Thu, 6 Apr 2000 16:35:21 +0530 Date: Thu, 6 Apr 2000 16:35:21 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: Marcelo Zaldini Hernandes cc: CCL Subject: Re: CCL:efrag on gamess ? In-Reply-To: <38C8FA94.98EC0648@npd.ufpe.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Marcelo, You may forward this "efrag on gamess" question to GAMESS user group: owner-gamess-users@Glue.umd.edu http://mineral.umd.edu/gamess-users Hope you will get help from them. With all the best, Tapan Ghanty ----------------------------------------------------------------------- On Fri, 10 Mar 2000, Marcelo Zaldini Hernandes wrote: > Dear all, > > I tried to do $EFRAG calculations whith gamess, using 49 H2Oef2 > water fragments, like: > > $efrag > coord=cart position=fixed > fragname=H2Oef2 > O1 2.0 1.0 3.0 > H2 3.4 2.1 3.4 > H3 4.2 4.5 5.2 > fragname=H2Oef2 > O1 7.0 3.0 3.0 > H2 1.4 5.1 3.4 > H3 2.2 1.5 5.2 > >. > >. > >. > $end > > When I ran a CHECK, received this message: > > ERROR! EFFECTIVE FRAGMENT $H2OEF2 NUMBER 1 DOES NOT MATCH STANDARD ONE. > > Anybody knows what it means ? > > Thanks in advance. > > -- > ************************************** > Marcelo Zaldini Hernandes > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Apr 6 09:35:29 2000 Received: from apollo.syrres.com (apollo.syrres.com [204.168.121.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA06933 for ; Thu, 6 Apr 2000 09:35:24 -0400 Received: from apollo.syrres.com ([204.168.121.242]) by apollo.syrres.com (Netscape Messaging Server 3.62) with SMTP id 207 for ; Thu, 6 Apr 2000 09:34:09 -0400 Received: from (pc-citra.syrres.com [204.168.121.167]) by apollo.syrres.com with SMTP (MailShield v1.5); Thu, 06 Apr 2000 09:34:09 -0400 Message-Id: <4.1.20000406083611.00921840@apollo.syrres.com> X-Sender: citra@apollo.syrres.com X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 06 Apr 2000 08:37:13 -0400 To: CHEMISTRY@ccl.net From: "Mario Citra" Subject: refractive index Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-SMTP-HELO: pc-citra X-SMTP-MAIL-FROM: citra@apollo.syrres.com X-SMTP-RCPT-TO: CHEMISTRY@ccl.net X-SMTP-PEER-INFO: pc-citra.syrres.com [204.168.121.167] Try the SPARC program at the following website: http://ibmlc2.chem.uga.edu/sparc Regards, Mario J. Citra Ph.D. Syracuse Research Corporation (315) 452-8406 citra@syrres.com From chemistry-request@server.ccl.net Thu Apr 6 15:42:19 2000 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA08409 for ; Thu, 6 Apr 2000 15:42:19 -0400 Received: from mail.chem.tamu.edu ([165.91.176.63]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Thu, 6 Apr 2000 14:50:56 -0500 Sender: jshen@ccl.net Message-ID: <38ECE8AD.D4DBAF56@mail.chem.tamu.edu> Date: Thu, 06 Apr 2000 12:42:37 -0700 From: Jingyi Shen Organization: TAMU X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:print MO coefficients in DMOL Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, All, I am a new user of DMOL program in InsightII from MSI. I did a calculation for a big molecule. I want to look at the MO coefficients in the output. Although I specified the program to print them, it did not print all of them. For each symmetry, it printed about 30 orbitals, but not include the one I am looking for. I use the keyword " Print eig psi", but don't know how to specify which MOs to print. I would appreciate any help from experienced DMOL users. Thanks in advance. Jingyi Shen TAMU From chemistry-request@server.ccl.net Thu Apr 6 15:26:22 2000 Received: from elsnycs18518.elsevier.com (elsnycs18518.elsevier.com [206.137.72.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA08327 for ; Thu, 6 Apr 2000 15:26:22 -0400 Received: from elsnycs18517.elsevier.com (unverified) by elsnycs18518.elsevier.com (Content Technologies SMTPRS 4.1.2) with ESMTP id for ; Thu, 6 Apr 2000 15:20:10 +0100 Received: from elsnycs18678.elsevier.com (exch.elsevier.com [206.137.75.31]) by elsnycs18517.elsevier.com (2.6 Build 1 (Berkeley 8.8.6)/8.8.4) with ESMTP id PAA00744 for ; Thu, 06 Apr 2000 15:22:40 -0400 Received: by exch.elsevier.com with Internet Mail Service (5.5.2448.0) id ; Thu, 6 Apr 2000 15:24:52 -0400 Message-ID: <7B2BD12DCFD0D211A3B70008C707D73B01432EB3@elsnycs18680.elsevier.com> From: "Glover, Jonathan (ELS)" To: "'chemistry@ccl.net'" Subject: Journal of Molecular Graphics and Modelling Date: Thu, 6 Apr 2000 15:22:13 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Dear CCL's: Just reminder that the Journal of Molecular Graphics and Modelling is available at a special subscription price of $65 for Members of the ACS Division of Computers in Chemistry (6 issues per year). Upcoming numbers of the journal include special issues on Advances in Modelling Carbohydrates, and Combinatorial Library Design. The journal also now includes an expanded News and Views section. For subscription information call 1-888-4ES-INFO, or e-mail usinfo-f@elsevier.com Jon Glover