From cmral@cluster2.urz.uni-halle.de Mon Jun 2 09:46:20 1997 Received: from mlucom3.urz.uni-halle.de for cmral@cluster2.urz.uni-halle.de by www.ccl.net (8.8.3/950822.1) id JAA21433; Mon, 2 Jun 1997 09:03:56 -0400 (EDT) From: Received: from cluster2.urz.uni-halle.de by mlucom3.urz.uni-halle.de with Local SMTP (PP); Mon, 2 Jun 1997 15:03:31 +0200 Received: by cluster2.urz.uni-halle.de (AIX 4.1/UCB 5.64/4.03) id AA39810; Mon, 2 Jun 1997 15:03:28 +0200 Message-Id: <9706021303.AA39810@cluster2.urz.uni-halle.de> Subject: once again, Looking for program To: CHEMISTRY@www.ccl.net Date: Mon, 2 Jun 1997 15:03:28 +0200 (MESZ) Cc: cmral@cluster2.urz.uni-halle.de (seifert) X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Dear colleagues, once again, I'll submit my question regarding the most efficient way of doing sophisticated post-HF calculations on quite largely TM-systems. I must me apologize for this second inquiry, but the reponses concerning my first submission last week cannot be received correctly because our mail server was run into problems. Many thanks Thomas ---------------- original message ---------------------------------- in order to examine the reliability of the DFT-treatment, I've been looking for the most efficient way of performing some calculations on our catalyst models with highly sophisticated single reference post-HF methods, such as CCSD[T], CPF or MCPF. A system under investigation is f.i. cationic NiC9H15 (C1-symmetry), consisting of 86 electrons within 246 basis functions. Which commercial program system should best be suitable of doing this large job regarding efficient consumption of cpu-time and storage space and possible restart facilities ? Any suggestions are highly appreciated. -- Thomas From chem8@york.ac.uk Tue Jun 3 01:46:26 1997 Received: from lendal.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id BAA26012; Tue, 3 Jun 1997 01:11:36 -0400 (EDT) Received: from ebor.york.ac.uk by lendal.york.ac.uk with SMTP (PP); Tue, 3 Jun 1997 06:09:52 +0100 Received: from localhost by ebor.york.ac.uk via SMTP (950511.SGI.8.6.12.PATCH526/951211.SGI) for id GAA16027; Tue, 3 Jun 1997 06:11:33 +0100 Date: Tue, 3 Jun 1997 06:11:33 +0100 (BST) From: John Waite To: chemistry@www.ccl.net Subject: Contact an SGI Computer Center Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters, I am interested in contacting any academic computer center that uses SGIs and services several groups/labs/departments to discuss the pros-and-cons of the use of their machine(s), in batch visa-vi background mode and as a parallel compared to a multi-task/processor computer. In particular, for running Computational Chemistry packages like Gauusian, Cadpac, Hondo and Molpro. Thanks, John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* Organic and Pharaceutical Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece From pino@jsbach.dichi.unina.it Tue Jun 3 12:46:33 1997 Received: from jsbach.dichi.unina.it for pino@jsbach.dichi.unina.it by www.ccl.net (8.8.3/950822.1) id LAA29574; Tue, 3 Jun 1997 11:54:04 -0400 (EDT) From: Received: by jsbach.dichi.unina.it (AIX 3.2/UCB 5.64/4.03) id AA07358; Wed, 28 Feb 1996 17:46:53 +0100 Date: Wed, 28 Feb 1996 17:46:53 +0100 Message-Id: <9602281646.AA07358@jsbach.dichi.unina.it> To: chemistry@www.ccl.net, govindan@chet.medc.umn.edu Subject: Re: CCL:AMBER chlorine parameters Please summarize =============================== Pino Milano Universita' degli Studi di Napoli e-mail pino@jsbach.dichi.unina.it ==================================== thanx in advance From pino@jsbach.dichi.unina.it Tue Jun 3 13:05:35 1997 Received: from jsbach.dichi.unina.it for pino@jsbach.dichi.unina.it by www.ccl.net (8.8.3/950822.1) id MAA29721; Tue, 3 Jun 1997 12:25:22 -0400 (EDT) From: Received: by jsbach.dichi.unina.it (AIX 3.2/UCB 5.64/4.03) id AA15867; Wed, 28 Feb 1996 18:19:49 +0100 Date: Wed, 28 Feb 1996 18:19:49 +0100 Message-Id: <9602281719.AA15867@jsbach.dichi.unina.it> To: chemistry@www.ccl.net Subject: benzene clusters I would appreciate to receive informations about benzene-containg Van der Waals complexes expecially with halogens and olefins, references , proper methods of calculation etc..... ============================================ Pino Milano Universita' degli Studi di Napoli Dipartimento di Chimica e-mail pino@jsbach.dichi.unina.it ============================================ Thanx in advance Pino From kostia@lcctoul.lcc-toulouse.fr Tue Jun 3 13:12:39 1997 Received: from lcctoul.lcc-toulouse.fr for kostia@lcctoul.lcc-toulouse.fr by www.ccl.net (8.8.3/950822.1) id LAA29638; Tue, 3 Jun 1997 11:58:22 -0400 (EDT) Received: from lcctoul.lcctoul.lcc-toulouse.fr ([192.70.112.77]) by lcctoul.lcc-toulouse.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id SAA16624 for ; Tue, 3 Jun 1997 18:03:50 -0700 Message-Id: <2.2.32.19970603155832.0067c4a0@lcctoul.lcc-toulouse.fr> X-Sender: kostia@lcctoul.lcc-toulouse.fr X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 03 Jun 1997 17:58:32 +0200 To: chemistry@www.ccl.net From: "Konstantin.Pokhodnya" Subject: Ni(dmit)2 Dear CCL Netters, I'm looking for a semi empirical program package or packages which allow to calculate an energetic structure as well as spectroscopic properties (IR, electronic spectra) of Ni with 1,3-dithiole-4,5 dithiolate (dmit) ligands in different oxidation states. I've tried, as the first step, to do calculate Ni(dmit)2 dianion using ZINDO/1 in 4.0 version of HyperChem but the results are strange. Thank you in advance , Best wishes, Konstantin From dqujfm0@PS.UIB.ES Tue Jun 3 13:18:06 1997 Received: from lofre for dqujfm0@PS.UIB.ES by www.ccl.net (8.8.3/950822.1) id LAA29613; Tue, 3 Jun 1997 11:56:42 -0400 (EDT) X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Tue, 3 Jun 1997 17:51:53 UTC+0100 Date: Tue, 3 Jun 1997 17:51:53 UTC+0100 X400-Originator: dqujfm0@PS.UIB.ES X400-Recipients: non-disclosure:; X400-Content-Type: P2-1984 (2) X400-MTS-Identifier: [/PRMD=iris/ADMD=mensatex/C=es/;970603175153] Content-Identifier: 380 From: Juan Frau To: chemistry@www.ccl.net Message-ID: <380*dqujfm0@PS.UIB.ES> Subject: Solvation in MM MIME-Version: 1.0 (Generated by Ean X.400 to MIME gateway) Content-Type: multipart/mixed; boundary="=_IF2cdze1" --=_IF2cdze1 Content-Type: text/plain; charset=US-ASCII Hi everybody I was wondering if someone has a list of different solvatin models used in molecular mechanics (and MC or MD) calculations. I am taking about explicit accountig for water molecules and continuum models (GB/SA in Macromodel for example). Could you send me this information or references related to? I 'll summarize the reply to the list Thanks. Juan Frau --=_IF2cdze1 Content-Type: text/plain; charset=US-ASCII ********************************************************************** Dr. Juan Frau Universitat Illes Balears Departament de Quimica Crta Valldemossa, km. 7.5 Palma de Mallorca- 07071 Spain Email: dqujfm0@ps.uib.es FAX: 34 71 17 34 26 ********************************************************************* --=_IF2cdze1 Content-Type: text/plain; charset=US-ASCII --=_IF2cdze1-- From Jeffrey.Gosper@brunel.ac.uk Tue Jun 3 13:23:35 1997 Received: from eros.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id LAA29560; Tue, 3 Jun 1997 11:51:52 -0400 (EDT) Received: from castjjg.brunel.ac.uk (actually chem-pc-03.brunel.ac.uk) by eros.brunel.ac.uk with SMTP (PP); Tue, 3 Jun 1997 16:44:05 +0100 Date: Tue, 3 Jun 1997 16:40:47 PDT From: Jeffrey Gosper Subject: Re: CCL:animation of presentation To: aiba cc: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Mon, 2 Jun 1997 11:59:43 +0200 aiba wrote: > From: aiba > Date: Mon, 2 Jun 1997 11:59:43 +0200 > Subject: CCL:animation of presentation > To: chemistry@www.ccl.net > > Dear Netters, > Two questions: > 1) Animation is desired for a talk which I am supposed > to present some time in August. Hints will be greately > appreciated about >... > -- Any hints about animation of molecular pictures > (i.e. visualisation of mol.-orbitals), of motion > of molecules, of animation of corresponding data > (like energy and other observables - parallely in > a separate window).. > -- what is better - to use LCD or video or big computer screen? I usually use Re_View/Netscape/Freelance graphics on a portable PC with an LCD display on an OHP. You'll need a high powered OHP to get the best results. Also the room must be darkened for the display to be effective. I have also used a very large SVGA screen, the results from this were superior. It all depends on the technology at your finger-tips and the size of the group your addressing. I use Re_View to animate chemical reactions. It includes a graphing facility such that plots of energy/geometry are available in an adjacent window. Selecting a point on the curve displays the corresponding 3D structure. The advantage of this method is that the input file is a simple multistructure XYZ file which can be readily generated. Using Netscape I can readily drive a presentation from the central screen. >2) Parallel question: to prepare a high-quality poster > what will be the most convenient software (win95/NT and Linux)?! I have used Corel draw and freelance graphics but Powerpoint is equally effective. >Getting/purchasing hardware/software isn't a problem for our group. (Lucky #####.) /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper, Dept. of Chemistry, BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187, facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's home page (molecular animations or Chem-4D): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From citra@syrres.com Tue Jun 3 14:46:33 1997 Received: from syrres.syrres.com for citra@syrres.com by www.ccl.net (8.8.3/950822.1) id OAA00399; Tue, 3 Jun 1997 14:07:57 -0400 (EDT) Date: Tue, 3 Jun 97 12:49 EST Message-ID: <9706031249.AA22778@syrres.syrres.com> Received: from syrres.com by syrres.syrres.com; Tue, 3 Jun 97 12:49 EST X-Sender: citra@srcinet.syrres.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Mario Citra Subject: MOPAC esp error I have tried to calculate the electrostatic potential charges on certain molecules using MOPAC 93. Although the program works fine for alkanes, alcohols etc. It outputs the message " Error from MOPAC: Program error in Electrostatic Potential" for certain classes of carbonyls. This problem has occured for certain aldehydes and carboxcylic acids, while esters, ketones and amides give no such error message and calculate the esp charges. This error occurs consistantly for ethanoic acid and acetaldehyde but does not seem to occur as more CH2 groups are added to the molecule. The problem is independent of the Hamiltonian employed. This is probably a bug in MOPAC, has anyone experienced this problem and know of any fixes? Regards, Mario J. Citra PhD Syracuse Research Corporation Merrill Lane Syracuse, New York 13210-4080 phone 315-426-3462 fax 315-426-3429 email citra@syrres.com Regards, Mario J. Citra PhD Syracuse Research Corporation Merrill Lane Syracuse, New York 13210-4080 phone 315-426-3462 fax 315-426-3429 email citra@syrres.com From orzenil@guarany.cpd.unb.br Tue Jun 3 17:46:35 1997 Received: from guarany.cpd.unb.br for orzenil@guarany.cpd.unb.br by www.ccl.net (8.8.3/950822.1) id RAA01157; Tue, 3 Jun 1997 17:04:38 -0400 (EDT) Received: by guarany.cpd.unb.br (AIX 3.2/UCB 5.64/4.03) id AA51196; Tue, 3 Jun 1997 18:02:25 -0300 Date: Tue, 3 Jun 1997 18:02:24 -0300 (GRNLNDST) From: "Orzenil Bonfim da Silva Junior]" To: CHEMISTRY@www.ccl.net Subject: QM / MM Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all , I am looking for any information about QM / MM calculations applied to biological systems with particular attention to the ligand-receptor interactions. I'll be very gratefull to anyone who could help me with references,web sites ... Thanks ... From XIENING@MEENA.CC.UREGINA.CA Tue Jun 3 18:46:36 1997 Received: from veena.cc.uregina.ca for XIENING@MEENA.CC.UREGINA.CA by www.ccl.net (8.8.3/950822.1) id SAA01462; Tue, 3 Jun 1997 18:44:54 -0400 (EDT) Received: from meena.cc.uregina.ca by meena.cc.uregina.ca (PMDF V5.1-8 #20153) id <01IJN4KXNVVKA0URV8@meena.cc.uregina.ca> for chemistry@www.ccl.net; Tue, 3 Jun 1997 16:44:43 CST Date: Tue, 03 Jun 1997 16:44:43 -0600 (CST) From: "XIE, NING" Subject: sulfur containing compounds To: chemistry@www.ccl.net Message-id: <01IJN4KXR3MAA0URV8@meena.cc.uregina.ca> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Hi, there, I need to calculate the energies of HOMO for some para-substituted phenyl methyl sulfides such as p-MeOPhSCH3, p-MePhSCH3, p-FPhSCH3, p-ClPhSCH3, p-NO2PhSCH3, PhSCH3 and their corresponding sulfoxides, and probably CH3SCH3 or (n-butyl)2S too. I have software like Gaussian 94 and Hyperchem at hand. I am wondering if someone can give me some suggestions that what kind of method (semi-empiracal or ab initio) and force field/basis set will work well with these compounds, I mean, give decent results? We tried HF/6-31G* and becke3LYP/6-31G* on two compounds and got quite different results (on Gaussian94). Any infomation is appreciated. Thank you for your time. I'll summerize the discussion. Diana From feng@mcs.anl.gov Tue Jun 3 19:46:35 1997 Received: from antares.mcs.anl.gov for feng@mcs.anl.gov by www.ccl.net (8.8.3/950822.1) id SAA01494; Tue, 3 Jun 1997 18:50:46 -0400 (EDT) Received: from bonnie.mcs.anl.gov (bonnie9.mcs.anl.gov [140.221.9.8]) by antares.mcs.anl.gov (8.6.10/8.6.10) with ESMTP id RAA06246 for ; Tue, 3 Jun 1997 17:50:48 -0500 From: Zhou Feng Date: Tue, 3 Jun 1997 17:50:45 -0500 Message-Id: <199706032250.RAA37844@bonnie.mcs.anl.gov> To: CHEMISTRY@www.ccl.net Subject: Re: CCL:QM / MM The QM/MM code developed by Dr. Paul Bash et al. for CHARMM may suite your needs. The code has been used extensively for enzyme reactions and energetics of protein--substrate interactions. Check PNAS v93 3698-3703 1996 or Biochemistry 1991, v30, pp 5826. Feng Zhou Post-doc Argonne Nat. Lab From zfeng@enzyme.bim.anl.gov Tue Jun 3 20:00:54 1997 Received: from enzyme.bim.anl.gov for zfeng@enzyme.bim.anl.gov by www.ccl.net (8.8.3/950822.1) id SAA01490; Tue, 3 Jun 1997 18:50:09 -0400 (EDT) Received: by enzyme.bim.anl.gov (AIX 3.2/UCB 5.64/4.03) id AA17733; Tue, 3 Jun 1997 17:50:11 -0500 Date: Tue, 3 Jun 1997 17:50:11 -0500 From: zfeng@enzyme.bim.anl.gov (Zhou Feng) Message-Id: <9706032250.AA17733@enzyme.bim.anl.gov> To: CHEMISTRY@www.ccl.net, orzenil@guarany.cpd.unb.br Subject: Re: CCL:QM / MM The QM/MM code developed by Dr. Paul Bash et al. for CHARMM may suite your needs. The code has been used extensively for enzyme reactions and energetics of protein--substrate interactions. Check PNAS v93 3698-3703 1996 or Biochemistry 1991, v30, pp 5826. Feng Zhou Post-doc Argonne Nat. Lab