From mdoyle@msi.com Wed Feb 18 04:21:09 1998 Received: from bioc1.msi.com for mdoyle@msi.com by www.ccl.net (8.8.3/950822.1) id DAA07284; Wed, 18 Feb 1998 03:37:59 -0500 (EST) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA02665; Wed, 18 Feb 98 00:36:53 -0800 Received: from unknown(146.202.0.106) by bioc1.msi.com via smap (V2.0) id xmaw02551; Wed, 18 Feb 98 00:36:21 -0800 Message-Id: <3.0.32.19980216180559.00705e2c@146.202.6.217> X-Sender: mdoyle@146.202.6.217 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 17 Feb 1998 00:34:39 -0800 To: "S. Roy Kimura" From: Michael Doyle Subject: Re: CCL:error bars on exptl solvation energies of AAs and ions? Cc: chemistry@www.ccl.net, srk@engpub1.bu.edu (S. Roy Kimura) Does anyone know a good online source of such data..... Michael Doyle At 07:50 PM 2/14/98 -0500, S. Roy Kimura wrote: >Hello, > >Does anyone know whether published experimental values of hydration >free energies of ions (e.g., Marcus, Biophys Chem 51(1994)111) and >amino-acid sidechain analogues (e.g., Wolfenden et al, Biochem >20(1981)849) have error bars associated with them? (they don't appear >in the above papers.) Do experimentalists have a way of estimating >these errors? Thanks. > >S. Roy Kimura >email: srk@bu.edu > >Molecular Engineering Research Laboratory >Boston University From root@liposome.genebee.msu.su Wed Feb 18 05:12:40 1998 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id EAA07475; Wed, 18 Feb 1998 04:36:48 -0500 (EST) Received: from localhost (root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) with SMTP id MAA16302; Wed, 18 Feb 1998 12:41:47 +0300 Date: Wed, 18 Feb 1998 12:41:47 +0300 (MSK) From: root To: Fenglou Mao cc: "CHEMISTRY@www.ccl.net" Subject: Re: CCL:Add Water to Proteins In-Reply-To: Message-ID: On Wed, 18 Feb 1998, Fenglou Mao wrote: > Hi, cclers, > Will anyone introduce any programs or papers about adding water > to proteins? > Thanks! http://www.imo.physik.uni-muenchen.de/~grubi/solvate/docu.html Regards, Eugene Leitl From yubofan@guomai.sh.cn Wed Feb 18 21:12:48 1998 Received: from guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id UAA12591; Wed, 18 Feb 1998 20:57:00 -0500 (EST) Received: from guomai.sh.cn ([202.96.224.229]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id JAA15224 for ; Thu, 19 Feb 1998 09:54:16 +0800 (CST) Message-ID: <34EB9097.D341778E@guomai.sh.cn> Date: Thu, 19 Feb 1998 09:53:27 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn Organization: Department of Chemistry, Fudan University X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: X-Ray format file Hi, I have got some X-Ray data file. I want to put the models' picture of the molecules into my Microsoft Word document on my PC. Is it possible? If it is possible, which PC software(Windows 95 / NT) can display these files by moncrystal model. Thank you very much. Y. Fan ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From yubofan@guomai.sh.cn Wed Feb 18 22:12:47 1998 Received: from guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id VAA12643; Wed, 18 Feb 1998 21:13:28 -0500 (EST) Received: from guomai.sh.cn ([202.96.225.137]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id KAA15882 for ; Thu, 19 Feb 1998 10:11:21 +0800 (CST) Message-ID: <34EB94A3.9DBA0A32@guomai.sh.cn> Date: Thu, 19 Feb 1998 10:10:43 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn Organization: Department of Chemistry, Fudan University X-Mailer: Mozilla 4.03 [en] (Win95; I) To: CHEMISTRY@www.ccl.net Subject: Structure of Compounds Containing Cadmium Hi, I have been doing the geometries of some molecules with Cd, so I need some structure datas. Can anybody give me some articles about compound containing Cd. Reviews are prefered. Thank you very much. Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From Halim.Guelzim@univ-lille1.fr Thu Feb 19 11:12:57 1998 Received: from lilserv.univ-lille1.fr for Halim.Guelzim@univ-lille1.fr by www.ccl.net (8.8.3/950822.1) id KAA15892; Thu, 19 Feb 1998 10:48:55 -0500 (EST) From: Received: from lip5rx.univ-lille1.fr (lip5rx.univ-lille1.fr [134.206.58.11]) by lilserv.univ-lille1.fr (8.8.7/jtpda-5.1) with SMTP id QAA15810 for ; Thu, 19 Feb 1998 16:48:44 +0100 (MET) Received: by lip5rx.univ-lille1.fr; id AA28629; Thu, 19 Feb 1998 16:48:40 +0100 Message-Id: <2.2f.32.19980219155554.00673b74@lip5rx.univ-lille1.fr> Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Feb 1998 16:55:54 +0100 To: chemistry@www.ccl.net Subject: khi-5 Hello! Dear collegues, we are studing some nonlinear effects related to khi5. We would like to now if some works were performed. From jkl@ccl.net Fri Feb 20 02:13:04 1998 Received: from ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id BAA25315; Fri, 20 Feb 1998 01:29:06 -0500 (EST) Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id BAA03752; Fri, 20 Feb 1998 01:29:01 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id BAA14320; Fri, 20 Feb 1998 01:29:00 -0500 (EST) Date: Fri, 20 Feb 1998 01:29:00 -0500 (EST) Message-Id: <199802200629.BAA14320@krakow.ccl.net> To: chemistry@www.ccl.net Subject: 98.06.06 Workshop: Molec. Modeling of Clays and Mineral Surfaces, Cleveland Cc: jkl@ccl.net Molecular Modeling of Clays and Mineral Surfaces ================================================ Saturday, June 6th - 8 AM to 6 PM Organized by James D. Kubicki (Computer Sciences Corp.) and W.F. Bleam (University of Wisconsin - Madison) Speakers: James Rustad (Pacific Northwest National Laboratories) Computational studies of mineral-water interfaces Neal Skipper (University College) Monte Carlo and molecular dynamics computer simulation of interlayer fluids Randy Cygan (Sandia National Laboratories) Molecular models of metal sorption on clay minerals Edward Tipping (Institute of Freshwater Ecology) Modeling the binding of protons and metal ions by humic substances In addition, there will be demonstrations by MSI, Inc. and Schrodinger, Inc. Workshop registration fee $95 (students, $45) before April 15; $105 (students, $50) after April 15. Registration fee will include course notes, continental breakfast, lunch and post-workshop reception. Limited to 100 registrants Details available at: http://www.cwru.edu/artsci/geol/files/cms.html ====================== Check also other conferences in CCL Archives: http://www.ccl.net/cca/info/conferencelist.html Jan Labanowski jkl@ccl.net From tamasgunda@tigris.klte.hu Fri Feb 20 03:13:06 1998 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id DAA26024; Fri, 20 Feb 1998 03:01:21 -0500 (EST) Message-Id: <199802200801.DAA26024@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Fri, 20 Feb 1998 08:50:49 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: yubofan@guomai.sh.cn Date: Fri, 20 Feb 1998 08:50:48 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:X-Ray format file CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Hi, > I have got some X-Ray data file. I want to put the models' picture of > the molecules into my Microsoft Word document on my PC. Is it possible? > > If it is possible, which PC software(Windows 95 / NT) can display these > files by moncrystal model. > > Thank you very much. > > Y. Fan > One possible solution: There is a molecule file comversion program Mol2mol (see www.compuchem.com/mol2mol.htm). It accepts general and major xray file formats and can transfrom it into many chemical file formats, thus practically you can move it into any modelling program working under Windows and then forward it to Word. best wishes Tamas ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 www.klte.hu/~gundat/gunda.htm H-4010 Debrecen Hungary ************************************************************************ From dinesh@medinst.ernet.in Fri Feb 20 04:13:17 1998 Received: from mahavir.doe.ernet.in for dinesh@medinst.ernet.in by www.ccl.net (8.8.3/950822.1) id DAA26356; Fri, 20 Feb 1998 03:57:52 -0500 (EST) Received: from vikram.doe.ernet.in by mahavir.doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA10889; Fri, 20 Feb 98 14:33:25+0530 Received: from medinst.UUCP by vikram.doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA27431; Fri, 20 Feb 98 14:35:36+050 From: DINESH BIOPHYSICS X-Mailer: SCO OpenServer Mail Release 5.0 To: chemistry@vikram!www.ccl.net Subject: RNA pred. Date: Fri, 20 Feb 98 9:57:14 IST Message-Id: <9802200957.aa16972@medinst.medinst.ernet.in> Hello Everybody, I am looking for freeware for predicting pseudoknots in RNA sequences. DOS, unix or SGI version will be preferable for me. Please reply, With Regards Dinesh Dinesh Gupta |||| ( oo ) +---------------------------------oooO (__) Oooo------------------------------+ Dinesh Gupta Molecular Modelling Lab. Department of Pathology All India Institute of Medical Sciences Ansari Nagar New Delhi 110029 INDIA e-mail: dinesh@medinst.ernet.in FAX : 91-11-6862663 +-----------------------------------------------------------------------------+ From Lutz.ACKERMANN@CALDCRD.elf-atochem.fr Fri Feb 20 04:20:02 1998 Received: from xr1-gw.atlas.fr for Lutz.ACKERMANN@CALDCRD.elf-atochem.fr by www.ccl.net (8.8.3/950822.1) id EAA26402; Fri, 20 Feb 1998 04:08:56 -0500 (EST) Message-Id: <199802200908.EAA26402@www.ccl.net> X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Fri, 20 Feb 1998 09:53:47 +0100 X400-Received: by mta xr1-gw.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Fri, 20 Feb 1998 09:53:47 +0100 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Fri, 20 Feb 1998 09:53:46 +0100 X400-Received: by /PRMD=ELF03/ADMD=ATLAS/C=FR/; Relayed; Thu, 19 Feb 1998 18:26:39 +0100 Date: Thu, 19 Feb 1998 18:26:39 +0100 X400-Originator: Lutz.ACKERMANN@CALDCRD.elf-atochem.fr X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=ELF03/ADMD=ATLAS/C=FR/;980219172639] X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: ACKERMANN Lutz GRL To: ccl Subject: AM1 under GAUSSIAN ??? Dear Netters, we have recently carried out a series of calculations using MOPAC/AM1. When we asked academic partners to do some ab initio calculations on the same set of compounds we were surprised to find, that there seems to be an inconcistency between GAUSSIAN/AM1 and MOPAC/AM1, concerning the heat capacity Cp. Does anyone know, if this is: -> a well known phenomenon/problem/bug -> a consequence of a different implementation (deliberate) or -> one of the great mysteries of life? For your orientation I have appended parts of the MOPAC and GAUSSIAN output of calcs for the CO2 molecule. Best Regards Lutz Ackermann _________________________________________________________ Dr. Lutz Ackermann Service Chimie Physique, Groupment de Recherches de Lacq elf atochem R.N 117, B.P. 34, F-64170 Lacq (France) Phone: (0033) 5 59 92 67 66 FAX: (0033) 5 59 92 67 65 e-mail: lutz.ackermann@CALDCRD.elf-atochem.fr or lutz@ri.ac.uk or phone/FAX: (0033) 5 59 27 65 43 lutz.ackermann@wanadoo.fr ___________________________________________________________ CO2 (AM1) MOPAC 6.0: ---------- CALCULATED THERMODYNAMIC PROPERTIES * TEMP. (K) PARTITION FUNCTION H.O.F. ENTHALPY HEAT CAPACITY ENTROPY KCAL/MOL CAL/MOLE CAL/K/MOL CAL/K/MOL 273 VIB. 1.139 203.06527 2.22755 1.00258 ROT. 255. 542.522 1.987 12.997 INT. 290. 745.587 4.215 14.000 TRA. 0.248E+27 1356.305 4.968 36.817 TOT. -80.062 2101.8922 9.1830 50.8170 298 VIB. 1.181 261.82494 2.46932 1.20837 ROT. 278. 592.203 1.987 13.172 INT. 328. 854.028 4.457 14.380 TRA. 0.282E+27 1480.509 4.968 37.252 TOT. -79.829 2334.5371 9.4247 51.6320 GAUSSIAN: -------- ... Energy= -0.127281006429 NIter= 9. ... E (Thermal) CV S KCAL/MOL CAL/MOL-KELVIN CAL/MOL-KELVIN TOTAL 9.040 7.411 51.623 ELECTRONIC 0.000 0.000 0.000 TRANSLATIONAL 0.889 2.981 37.270 ROTATIONAL 0.592 1.987 13.171 VIBRATIONAL 7.559 2.443 1.182 VIBRATION 1 0.886 1.182 0.586 VIBRATION 2 0.887 1.179 0.583 ... Transforming the Energy given by GAUSSIAN from Hartree to kcal/mol, one gets -79.8653 kcal/mol, which is close to the Heat of Formation calculated from MOPAC (at 298K), -79.829 kcal/mol. The entropy is also very similar between the two programs, but the heat capacity differs a lot ( 7.411 CAL/MOL-KELVIN in GAUSSIAN vs. 9.4247 CAL/K/MOL in MOPAC!!??? From tschilli@pils.physik.TU-Berlin.DE Fri Feb 20 07:13:08 1998 Received: from mail.zrz.TU-Berlin.DE for tschilli@pils.physik.TU-Berlin.DE by www.ccl.net (8.8.3/950822.1) id GAA26830; Fri, 20 Feb 1998 06:23:34 -0500 (EST) Received: from pils.physik.TU-Berlin.DE by mail.zrz.TU-Berlin.DE with SMTP (IC-PP); Fri, 20 Feb 1998 12:23:13 +0100 Received: from localhost by pils.physik.TU-Berlin.DE (8.8.8/ZRZ-Gen) id LAA03639; Fri, 20 Feb 1998 11:23:10 GMT Date: Fri, 20 Feb 1998 12:23:09 +0100 (MET) From: Tanja Schilling To: chemistry@www.ccl.net Subject: CCL: Dynamics of excited molecules Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Where could I find information on methods of calculating what happens to a molecule (of about 20 atoms) when a certain ammount of energy is pumped into it instantaniously, which states are excited, which fragments it will probably break into? Thanks Tanja Schilling Institut fuer Astronomie und Astrophysik TU-Berlin tschilli@pils.physik.tu-berlin.de From pino@jsbach.dichi.unina.it Fri Feb 20 07:24:43 1998 Received: from jsbach.dichi.unina.it for pino@jsbach.dichi.unina.it by www.ccl.net (8.8.3/950822.1) id GAA26907; Fri, 20 Feb 1998 06:46:45 -0500 (EST) From: Received: by jsbach.dichi.unina.it (AIX 3.2/UCB 5.64/4.03) id AA19434; Mon, 4 Jul 1994 12:38:54 GMT Date: Mon, 4 Jul 1994 12:38:54 GMT Message-Id: <9407041238.AA19434@jsbach.dichi.unina.it> To: chemistry@www.ccl.net Subject: semi-empirical parameters for Mg Dear Netters, My friend would like to know something about semi-empirical parameters of Mg. The PM3 understimates the bond lenght Mg-X (for example in Mg-Cl2 the PM3 computed distance Mg-Cl is 1.887, while the experimental one is 2.186. In some complexes the Mg-O PM3 distance is about 1.87 but the experimental ones are about 2.10. Are there AM1 parameters for Mg atom or refined from original reference of PM3 ( J. Comp. Chem. 1991) which works better for these kind of systems ? Thanks in advance Pino Milano ========================= Pino Milano University of Salerno e-mail pino@jsbach.dichi.unina.it ========================= From rvenable@deimos.cber.nih.gov Fri Feb 20 13:13:11 1998 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id MAA29839; Fri, 20 Feb 1998 12:34:08 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA093195919; Fri, 20 Feb 1998 12:31:59 -0500 Date: Fri, 20 Feb 1998 12:31:59 -0500 (EST) From: Rick Venable To: root Cc: Fenglou Mao , "CHEMISTRY@www.ccl.net" Subject: Re: CCL:Re: CCL:Add Water to Proteins In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > On Wed, 18 Feb 1998, Fenglou Mao wrote: > > Hi, cclers, > > Will anyone introduce any programs or papers about adding water > > to proteins? On Wed, 18 Feb 1998, root wrote: > http://www.imo.physik.uni-muenchen.de/~grubi/solvate/docu.html > > Regards, > Eugene Leitl Of course, this makes that sphere of waters, with all it's limitations (see my contribution from last Saturday). Is there anything similar for other shapes, e.g. dodecahedrons or truncated octahedrons? -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable From seabra@NPD.UFPE.BR Fri Feb 20 14:13:10 1998 Received: from NPD1.NPD.UFPE.BR for seabra@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id OAA00466; Fri, 20 Feb 1998 14:05:08 -0500 (EST) Received: from danon (danon.dqf.ufpe.br) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01ITT4F5CXNK000FZH@NPD.UFPE.BR> for CHEMISTRY@www.ccl.net; Fri, 20 Feb 1998 16:04:38 GMT-3 Date: Fri, 20 Feb 1998 16:13:16 -0300 From: Gustavo de Miranda Seabra Subject: Re: CCL:G:AM1 under GAUSSIAN ??? To: ACKERMANN Lutz GRL , ccl Message-id: <002801bd3e33$991b7690$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mimeole: Produced By Microsoft MimeOLE V4.72.2106.4 I have seen a problem like this once. I feel that the structure optimization of GAUSSIAN is much better tham of MOPAC. In fact, the problem I have seen is about structure optimizaton and, while most times MOPAC made just a little change on the structure (but reaching a local minimum fast), GAUSSIAN moved completely the structure, taking more time but reaching much better structures. -----Original Message----- From: ACKERMANN Lutz GRL To: ccl Date: Friday, February 20, 1998 6:14 AM Subject: CCL:G:AM1 under GAUSSIAN ??? > > >Dear Netters, >we have recently carried out a series of calculations >using MOPAC/AM1. When we asked academic partners to do some ab initio >calculations on the same set of compounds we were surprised to find, that >there >seems to be an inconcistency between GAUSSIAN/AM1 and MOPAC/AM1, >concerning the heat capacity Cp. Does anyone know, if this is: > -> a well known phenomenon/problem/bug > -> a consequence of a different implementation (deliberate) or > -> one of the great mysteries of life? > >For your orientation I have appended parts of the MOPAC and GAUSSIAN output >of calcs for the CO2 molecule. > > >Best Regards > >Lutz Ackermann > > >_________________________________________________________ >Dr. Lutz Ackermann > >Service Chimie Physique, Groupment de Recherches de Lacq >elf atochem >R.N 117, B.P. 34, F-64170 Lacq (France) >Phone: (0033) 5 59 92 67 66 FAX: (0033) 5 59 92 67 65 >e-mail: lutz.ackermann@CALDCRD.elf-atochem.fr or lutz@ri.ac.uk > >or > >phone/FAX: (0033) 5 59 27 65 43 >lutz.ackermann@wanadoo.fr >___________________________________________________________ > > >CO2 (AM1) > > >MOPAC 6.0: > ---------- > CALCULATED THERMODYNAMIC PROPERTIES > * > TEMP. (K) PARTITION FUNCTION H.O.F. ENTHALPY HEAT CAPACITY > ENTROPY > KCAL/MOL CAL/MOLE CAL/K/MOL > CAL/K/MOL > > 273 VIB. 1.139 203.06527 2.22755 > 1.00258 > ROT. 255. 542.522 1.987 > 12.997 > INT. 290. 745.587 4.215 > 14.000 > TRA. 0.248E+27 1356.305 4.968 > 36.817 > TOT. -80.062 2101.8922 9.1830 > 50.8170 > > 298 VIB. 1.181 261.82494 2.46932 > 1.20837 > ROT. 278. 592.203 1.987 13.172 > INT. 328. 854.028 4.457 14.380 > TRA. 0.282E+27 1480.509 4.968 37.252 > TOT. -79.829 2334.5371 9.4247 51.6320 > > > > > > >GAUSSIAN: > -------- > > ... > >Energy= -0.127281006429 NIter= 9. > > ... > > E (Thermal) CV S > KCAL/MOL CAL/MOL-KELVIN CAL/MOL-KELVIN > TOTAL 9.040 7.411 51.623 > ELECTRONIC 0.000 0.000 0.000 > TRANSLATIONAL 0.889 2.981 37.270 > ROTATIONAL 0.592 1.987 13.171 > VIBRATIONAL 7.559 2.443 1.182 > VIBRATION 1 0.886 1.182 0.586 > VIBRATION 2 0.887 1.179 0.583 > ... > > > >Transforming the Energy given by GAUSSIAN from Hartree to kcal/mol, one >gets -79.8653 kcal/mol, which is close to the Heat of Formation calculated >from MOPAC (at 298K), -79.829 kcal/mol. The entropy is also very similar >between >the two programs, but the heat capacity differs a lot ( 7.411 CAL/MOL-KELVIN >in >GAUSSIAN vs. 9.4247 CAL/K/MOL in MOPAC!!??? > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: Lutz.ACKERMANN@CALDCRD.elf-atochem.fr >-- Original Sender From: Address: Lutz.ACKERMANN@CALDCRD.elf-atochem.fr >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 genghis@darkwing.uoregon.edu Fri Feb 20 16:13:15 1998 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id PAA00907; Fri, 20 Feb 1998 15:22:05 -0500 (EST) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.8/8.8.8) with SMTP id MAA04437 for ; Fri, 20 Feb 1998 12:22:03 -0800 (PST) Date: Fri, 20 Feb 1998 12:22:03 -0800 (PST) From: "Dale A. Braden" To: cclpost Subject: PC configuration for QM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I've looked at the CCL archives for info on this question, but the most up-to-date advice is important. I'm going to set up a PC/Linux system for doing quantum chemical calculations (probably using Q-Chem and Red Hat Linux 5.0), and the question is, What sort of hardware should I buy? Rather than ask for answers to this broad question, I'd like to suggest a system and solicit criticisms of it. Here goes: I plan on getting a dual-cpu PentiumII 333Mhz motherboard (these have the usual 512K L2 cache), 128Mb SDRAM, and two ultrawide SCSI drives (as large and as fast as can be supported-- any recommendations here?). Graphical capability is less of a concern, because I won't be using graphical interfaces to the QM software. Tyan and Supermicro supply the motherboards, and I'd probably go to Adaptec for the SCSI drives. A system built around an Alpha chip is also a possibility, but I'm not sure whether the Alpha is going to be developed any further, and I don't know about compatibility issues between software, Linux, peripherals, and the Alpha chip. Also, I will probably have to install WindowsNT or '98 on this system in order to use the usual word processing/spreadsheet stuff, but I don't think this works with the Alpha architecture. Any pitfalls I should be aware of, or special devices I should consider? I'll certainly get the proper power supply and cooling fans for the system. Best wishes to all, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From destack@unomaha.edu Fri Feb 20 18:13:12 1998 Received: from s-cwis.unomaha.edu for destack@unomaha.edu by www.ccl.net (8.8.3/950822.1) id RAA02011; Fri, 20 Feb 1998 17:25:12 -0500 (EST) Received: from cas.unomaha.edu (cas.unomaha.edu [137.48.34.40]) by s-cwis.unomaha.edu (8.8.5/8.8.5) with ESMTP id QAA26796 for ; Fri, 20 Feb 1998 16:21:12 -0600 (CST) Received: from CAS/MAILQUEUE by cas.unomaha.edu (Mercury 1.21); 20 Feb 98 16:25:16 -600 Received: from MAILQUEUE by CAS (Mercury 1.21); 20 Feb 98 16:24:50 -600 Received: from zinc.unomaha.edu by cas.unomaha.edu (Mercury 1.21); 20 Feb 98 16:24:49 -600 Received: by zinc.unomaha.edu with Microsoft Mail id <01BD3E1C.5D6E2D70@zinc.unomaha.edu>; Fri, 20 Feb 1998 16:26:58 -0600 Message-ID: <01BD3E1C.5D6E2D70@zinc.unomaha.edu> From: "Douglas E. Stack" To: "'CCL'" Subject: Guideline for large servers Date: Fri, 20 Feb 1998 16:26:57 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear CCLers, Our University as recently started installing a new SGI Onyx2 server. = I'm am part of a committee who's immediate goal to establish user polices for this large server (or mini super computer, = I haven't decide what class it in). If anyone on the list has experince = handling the needs of users on a large server it would greatly = appreicated. The following items came to mind during our recent = meeting: 1) What criteria should be used in issuing an account? 2) What groups (user groups) can be made so that future CPU priorities = can established? 3) What guidelines can be established for submitting computationally = intensive jobs 4) Other areas we haven't considered. Our idea is to produce a one to two page document that can be given to = new users outlining the polices. Does anyone have such a document? If = so, attach a copy and email to me if you don't mind. I'd like to get as = many ideas on as many issues as possible. Thanks in advance, Douglas E. Stack=09 Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3888 (fax) destack@unomaha.edu