From chemistry-request@server.ccl.net Thu Feb 22 18:24:35 2001 Received: from hotmail.com (f24.law10.hotmail.com [64.4.15.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1MNOYw28056 for ; Thu, 22 Feb 2001 18:24:34 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 22 Feb 2001 15:22:39 -0800 Received: from 128.97.139.222 by lw10fd.law10.hotmail.msn.com with HTTP; Thu, 22 Feb 2001 23:22:39 GMT X-Originating-IP: [128.97.139.222] From: "hu eric" To: chemistry@ccl.net Subject: htmldoc Date: Thu, 22 Feb 2001 15:22:39 -0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 22 Feb 2001 23:22:39.0252 (UTC) FILETIME=[58EB7D40:01C09D26] Hi, CCLers It seems to me that htmldoc can only turn one html page to pdf and exclude jpeg pictures(unless a local html). Did anyone say that it can include all the hotlinks in that html page when making one pdf file? Thanks. Eric _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Thu Feb 22 21:05:35 2001 Received: from smtp.263.net ([202.96.44.19]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1N25Rw29040 for ; Thu, 22 Feb 2001 21:05:28 -0500 Received: from Frank (unknown [202.120.99.151]) by smtp.263.net (Postfix) with ESMTP id 298121C910BCA for ; Fri, 23 Feb 2001 10:07:03 +0800 (CST) Message-ID: <000e01c09d3b$99f25240$976378ca@ecust.edu.cn> From: "Yuan Qin" To: Subject: Second virial coefficient from simulations? Date: Fri, 23 Feb 2001 09:54:43 +0800 You can refer this paper: Monte carlo calculation of the osmotic second virial coefficient of off lattice athermal polymers. A. Yethiraj et al. Macromolecules, 25, 3979 (1992) Qin Yuan > > > Thanks, but I don't quite understand what you mean. Do you mean a > simulation of the polymer? What do I measure during the simulation? > > K > > > > From: "qinyuan" > X-Priority: 3 > X-Originating-IP: [202.120.99.151] > > You can use Monte Carlo calculation. > > > > > > > > > > > > >I would like to estimate the second virial coefficient for a simple > >polymer computer model I've devised. The analytic calculation is hard > >to do because the potential energy function for the system includes an > >implicit term coming from the SHAKE algorithm that enforces the length > >constraints. The system now models a single chain in vacuo. > > > >If someone knows how one computes the the second virial from > >simulation data, (or else where I can read how to do it), please let > >me know. > > > >Regards, > > > >KJ From chemistry-request@server.ccl.net Thu Feb 22 21:25:47 2001 Received: from lacebark.ntu.edu.au ([138.80.63.12]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1N2Piw29103 for ; Thu, 22 Feb 2001 21:25:45 -0500 Received: (qmail 22968 invoked by uid 200); 23 Feb 2001 11:40:27 +0930 Date: Fri, 23 Feb 2001 11:40:27 +0930 From: Brian Salter-Duke To: "'CCL'" Subject: Re: CCL:ferric ion Message-ID: <20010223114026.A14227@lacebark.ntu.edu.au> Mail-Followup-To: 'CCL' References: <157A51F55AAAD3119CD70008C7B1629DDAACCD@lvlxch01.unitedcatalysts.com> Mime-Version: 1.0 Content-Type: text/plain; charset=IBM-850 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.3.10i In-Reply-To: <157A51F55AAAD3119CD70008C7B1629DDAACCD@lvlxch01.unitedcatalysts.com>; from dshobe@sud-chemieinc.com on Thu, Feb 22, 2001 at 04:35:06PM -0500 On Thu, Feb 22, 2001 at 04:35:06PM -0500, Shobe, Dave wrote: > The CBS methods are only available for elements H - Cl. These methods use > several esoteric basis sets, and parameterizing new ones for Fe would be a > lot of work, so I doubt anyone's done it. I don't think any "black box" > quantum mechanical methods have been developed for the transition metals, > since there are too many problems with SCF convergence, low-lying excited > states of various spin multiplicities, multiple determinants with > significant contribution to the wave function, etc. > > Let me know if any of the above is wrong--I'd be very interested (at least > if the method is any good :-) I agree with the above in general. However, we (Ramakrishna and Duke) have extended the CBS methods to the elements Ga - Br. We reported these results at the Pacifichem 2000 meeting last December and the paper is curently with the referees. Gaussian have indicated that they will include the extension in G98, but I am holding up sending them the details until the paper is at least accepted. Regards, Brian Duke. > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > > > -----Original Message----- > From: Dr. Daniel Glossman [mailto:glossman@cimav.edu.mx] > Sent: Wednesday, February 21, 2001 2:00 PM > To: Computational Chemistry List > Subject: CCL:ferric ion > > > Dear netters: > > Is there anybody who has been succesful in calculating the > the energy of ferric ion (Fe+3) with the CBS-QB3 compound > method? How the input should be? > > Thanks in advance > > Dr. Daniel Glossman Mitnik > > ************************************************************************** > Dr. Daniel Glossman Mitnik > Centro de Investigacion en Materiales Avanzados (CIMAV) > LAQUICOM - Laboratorio de Química Computacional > Miguel de Cervantes 120 > Complejo Industrial Chihuahua > Chihuahua, Chih. 31109 > Mexico > Phone: (52) 14 391151 FAX: (52) 14 391112 > E-mail: glossman@mail.cimav.edu.mx > glossman@hotmail.com > dglossman@yahoo.com > ************************************************************************** > > > > > > > > > > > -= 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 > > > > -- Associate Professor Brian Salter-Duke (Brian Duke) b_duke@lacebark.ntu.edu.au Chemistry, School of BECS, SITE, NT University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847. http://www.smps.ntu.edu.au/ Get PGP2 Key:- http://www.smps.ntu.edu.au/chemistry/duke.key.html From chemistry-request@server.ccl.net Thu Feb 22 21:33:29 2001 Received: from pn2.vsnl.net.in (pn2.vsnl.net.in [202.54.10.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1N2XRw29131 for ; Thu, 22 Feb 2001 21:33:28 -0500 Received: from pn2.vsnl.net.in ([203.199.131.15]) by pn2.vsnl.net.in (8.9.0/8.9.0) with ESMTP id HAA00569; Fri, 23 Feb 2001 07:59:46 +0530 (IST) Message-ID: <3A95D068.D2A2000A@pn2.vsnl.net.in> Date: Fri, 23 Feb 2001 08:22:24 +0530 From: "Dr. Gadres" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: Jochen =?iso-8859-1?Q?K=FCpper?= , CHEMISTRY@server.ccl.net Subject: Re: CCL:Dimers of furan, pyrrole and thiophene.. References: <3A671282.2E76CB96@pn2.vsnl.net.in> <20010119142512.C2360888@compchem.dfh.dk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All : Here is the only answer I received to the query on dimers of furan, pyrrole and thiophene posted on my behalf.............Shridhar Gadre > > Dear Sirs : > > It is well-known that benzene dimer has two possible geometries. > > One of these is T-shaped where one benzene molecule is > > perpendicular to the othe other one. The other is the so-called shifted > parallel > one. Is there something known about the dimers of thiophene, > furan > > and pyrrole molecules? Any references will be greatly appreciated. > > Thanks in anticipation!.........................students of Professor > Gadre > Jeremy Greenwood wrote: > I recently had a look at a letter in JACS > (from the web, not out in print yet,10.1021/ja003256d) > Sonya L McKay, Brandy Haptonstall and Samuel H Gellman > Beyond the Hydrophobic Effect: Attractions Involving Heteroaromatic > Rings in Aqueous Solution > where they use NMR anaylsis to look at the effect of heteroatoms > on pi-stacking. Not exactly what you are looking for though. > > I look forward with interest to a summary of responses to this > important question. > > Best wishes, > > Jeremy > ---------------------------------------------------------------------- > Jeremy Greenwood jeremy.greenwood@i.am > Department of Medicinal Chemistry bh +45 35306117 > Royal Danish School of Pharmacy fx +45 35306040 > Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 > ---------------------------------------------------------------------- > Nothing cures insomnia like the realisation that it's time to get up. > ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Feb 23 03:37:40 2001 Received: from gate.syntem-sa.fr (gate.syntem-sa.fr [146.19.248.65]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1N8bdw31063 for ; Fri, 23 Feb 2001 03:37:39 -0500 Received: (from uucp@localhost) by gate.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) id JAA58191 for <@firewall.syntem-sa.fr:chemistry@ccl.net>; Fri, 23 Feb 2001 09:34:44 +0100 (MET) Received: from syntem-sa.fr(10.0.0.2) by gate.syntem-sa.fr via smap (4.1) id xma058274; Fri, 23 Feb 01 09:34:42 +0100 Received: from victoria.syntem-sa.fr (victoria.syntem-sa.fr [10.0.0.44]) by laetitia.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA04628 for <@laetitia.syntem-sa.fr:chemistry@ccl.net>; Fri, 23 Feb 2001 09:32:09 +0100 (MET) Received: from syntem-sa.fr (localhost [127.0.0.1]) by victoria.syntem-sa.fr (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA17565 for ; Fri, 23 Feb 2001 09:37:48 +0100 (MET) Sender: dturner@syntem-sa.fr Message-ID: <3A96215C.9BC1B24@syntem-sa.fr> Date: Fri, 23 Feb 2001 09:37:48 +0100 From: David Turner Reply-To: dturner@syntem.com Organization: Computational Drug Design, Syntem X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: Protease Inhibitors Entropy/Enthalpy References: <3A957139.F564083B@yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Can anybody point me to an article or articles discussing the relative contributions of entropic and enthalpic terms to the free energy of binding of substrates and/or inhibitors of HIV protease or perhaps in more general terms for aspartic and the various other classes of proteases? Thanks Dave -- ________________________________________________________________ David Turner Synt:em Senior Modeling Scientist Parc Scientifique G.Besse Computational Drug Discovery 30000 Nimes email: dturner@syntem.com France Tel: Switchboard: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 Direct Line: +33 (0)4 66 04 22 85 ________________________________________________________________ Discover New Drugs, Discover Synt:em http://www.syntem.com ________________________________________________________________ From chemistry-request@server.ccl.net Fri Feb 23 01:09:00 2001 Received: from cascara.UVic.CA (root@cascara.uvic.ca [142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1N690w30092 for ; Fri, 23 Feb 2001 01:09:00 -0500 Received: from p17-5.dialup.uvic.ca (p17-5.dialup.uvic.ca [142.104.17.5]) by cascara.UVic.CA (8.11.2/8.11.2) with SMTP id f1N692d153836; Thu, 22 Feb 2001 22:09:02 -0800 From: Roy Jensen To: Max Cc: chemistry@ccl.net Subject: Re: CCL:"Big"jobs on Quantum Chemsitry in Linux plataform Date: Thu, 22 Feb 2001 22:12:35 -0800 Message-ID: References: <3A957139.F564083B@yahoo.com> In-Reply-To: <3A957139.F564083B@yahoo.com> X-Mailer: Forte Agent 1.8/32.548 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f1N690w30093 I have observed the same problem with Gaussian 98W. The error occurred with some CIS calculations on diatomic rhodium molecules. I appear to have deleted the output files. I have not come up with a work around. Roy Jensen > The problem with the jobs is that frecuently there is a "nan" result on > the MP2-energy, or the somewhere elseearlier in the computation, and the > job doen't finish well-behaved. > > The 800MHz machine has 1GB in RAM, and enough disk to perform the > computation, and it does perform it complete, but with this kind of > output in gaussian, as an example > > 5,148.878,0\H,25,1.085054,23,110.165,17,-185.198,0\H,25,1.086148,23,11 > 0.493,17,54.162,0\H,25,1.086712,23,109.841,17,-65.099,0\\Version=x86-L > inux-G98RevA.7\HF=-570.9295579\MP2=nan\RMSD=7.238e-10\PG=C01 [X(C8H16N > 2O2)]\\@ > > The same kind of results comes from Gamess, or NWchem. Most of the > times, the "nan" is in the SCF optimization cycle : > > Cycle 7 Pass 1 IDiag 1: > RMSU= 9.43D-07 CP: 1.00D+00 1.24D+00 > E=-0.105688403862277D+04 Delta-E= -0.000000057351 > DIIS: error= 1.53D-05 at cycle 3. > Coeff: 0.486D+00-0.688D-02-0.148D+01 > RMSDP=1.60D-06 MaxDP=4.70D-05 > > Cycle 8 Pass 1 IDiag 1: > RMSU= 4.05D-07 CP: 1.00D+00 1.86D+00 1.69D+00 > E= -nan Delta-E= -nan > DIIS: error= nan at cycle 4. > RMSDP=2.65D-01 MaxDP=1.80D+01 > > > I would like to know if this sames behavoir is observed in any other > group using linux on Intel arquitecture. > > Please Send any comment to maxvaldez@yahoo.com, since i'm still waiting > my confirmation to the CCL subscription. > > Max > p.s. sorry for my english From chemistry-request@server.ccl.net Fri Feb 23 05:35:17 2001 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1NAYow31719 for ; Fri, 23 Feb 2001 05:35:02 -0500 Received: from fenII-121 (fenII-121.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with SMTP id MAA02555; Fri, 23 Feb 2001 12:30:23 +0200 (EET) Message-Id: <3.0.2.32.20010223123033.006b76b4@century.fen.bilkent.edu.tr> X-Sender: salzner@century.fen.bilkent.edu.tr X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Fri, 23 Feb 2001 12:30:33 +0200 To: "Dr. Gadres" From: Ulrike Salzner Subject: Re: CCL:Dimers of furan, pyrrole and thiophene.. Cc: chemistry@ccl.net In-Reply-To: <3A95D068.D2A2000A@pn2.vsnl.net.in> References: <3A671282.2E76CB96@pn2.vsnl.net.in> <20010119142512.C2360888@compchem.dfh.dk> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 08:22 23.02.2001 +0530, you wrote: >Dear All : Here is the only answer I received to the query on dimers of furan, > >pyrrole and thiophene posted on my behalf.............Shridhar Gadre Dear Sir, I saw your question but did not feel entitled to reply since I am only a woman. Maybe you realize that ingnoring women throws away half the brain power of human kind! Bithiophene has been studied experimentally and theoretically. It is non-planar in the gas phase and planar in the crystal(anti conformation). Syn and anti conformations have been observed with NMR and the energy difference is about 0.2 kcal/mol. See: C. Aleman and L. Julia, J. Phys. Chem. 1996, 100, 14661-14664 and references therein. Sincerely, Ulrike Salzner > >> > Dear Sirs : >> > It is well-known that benzene dimer has two possible geometries. >> > One of these is T-shaped where one benzene molecule is >> > perpendicular to the othe other one. The other is the so-called shifted >> parallel > one. Is there something known about the dimers of thiophene, >> furan >> > and pyrrole molecules? Any references will be greatly appreciated. >> > Thanks in anticipation!.........................students of Professor >> Gadre >> Jeremy Greenwood wrote: >> I recently had a look at a letter in JACS >> (from the web, not out in print yet,10.1021/ja003256d) >> Sonya L McKay, Brandy Haptonstall and Samuel H Gellman >> Beyond the Hydrophobic Effect: Attractions Involving Heteroaromatic >> Rings in Aqueous Solution >> where they use NMR anaylsis to look at the effect of heteroatoms >> on pi-stacking. Not exactly what you are looking for though. >> >> I look forward with interest to a summary of responses to this >> important question. >> >> Best wishes, >> >> Jeremy >> ---------------------------------------------------------------------- >> Jeremy Greenwood jeremy.greenwood@i.am >> Department of Medicinal Chemistry bh +45 35306117 >> Royal Danish School of Pharmacy fx +45 35306040 >> Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 >> ---------------------------------------------------------------------- >> Nothing cures insomnia like the realisation that it's time to get up. >> ---------------------------------------------------------------------- > > > >-= 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 > > > > > > > Dr. Ulrike Salzner e-mail:salzner@fen.bilkent.edu.tr Associate Professor Tel.: 90-312-290-2122 Department of Chemistry Fax.: 90-312-266-5097 Bilkent University 06533 Bilkent, Ankara,Turkey From chemistry-request@server.ccl.net Fri Feb 23 11:13:52 2001 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1NGDqw01847 for ; Fri, 23 Feb 2001 11:13:52 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id IAA18860; Fri, 23 Feb 2001 08:13:55 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id IAA00487; Fri, 23 Feb 2001 08:13:55 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3A968C42.5F4382A9@usc.edu> Date: Fri, 23 Feb 2001 08:13:54 -0800 From: Jordi Villa To: David Turner CC: Computational Chemistry List Subject: Re: CCL:Protease Inhibitors Entropy/Enthalpy References: <3A957139.F564083B@yahoo.com> <3A96215C.9BC1B24@syntem-sa.fr> Check, Proteins: Structure, Function, and Genetics Volume 39, Issue 4, 2000. Pages: 393-407 Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease Yuk Yin Sham, Zhen Tao Chu, Holly Tao, Arieh Warshel * You can get it from the web at: http://www3.interscience.wiley.com/cgi-bin/abstract/72501371/START David Turner wrote: > Hi > > Can anybody point me to an article or articles discussing the > relative contributions of entropic and enthalpic terms to the > free energy of binding of substrates and/or inhibitors of HIV > protease or perhaps in more general terms for aspartic and the > various other classes of proteases? > > Thanks > > Dave > > -- > > ________________________________________________________________ > > David Turner Synt:em > Senior Modeling Scientist Parc Scientifique G.Besse > Computational Drug Discovery 30000 Nimes > email: dturner@syntem.com France > > Tel: > Switchboard: +33 (0)4 66 04 86 66 Fax: +33 (0)4 66 04 86 67 > Direct Line: +33 (0)4 66 04 22 85 > ________________________________________________________________ > > Discover New Drugs, Discover Synt:em > http://www.syntem.com > ________________________________________________________________ > -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 From chemistry-request@server.ccl.net Fri Feb 23 11:36:25 2001 Received: from iris.chimfarm.unipg.it (iris.chimfarm.unipg.it [141.250.13.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1NGaOw01959 for ; Fri, 23 Feb 2001 11:36:24 -0500 Received: from cost.chimfarm.unipg.it ([141.250.13.14] helo=cost) by iris.chimfarm.unipg.it with smtp (Exim 2.04 #2) id 0tq8to-0001nM-00 for chemistry@ccl.net; Fri, 23 Feb 1996 17:35:48 -0800 Message-ID: <002d01c09db6$9141ef40$0e0dfa8d@chimfarm.unipg.it> From: "Mirco Meniconi" To: Subject: Date: Fri, 23 Feb 2001 17:35:01 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 I have a problem with Sybyl's visualization on the linux terminal (I have installed on my computer a red-hat7 distribution) the error message from my linux terminal is: "picking not supported" how can I do? tanks in advance Mirco -------------------------------------------------------- Mirco Meniconi Dipartimento di chimica e tecnologia del farmaco Via elce di sotto n. 1 06100 Perugia (Italy) Email: mirco.me@inwind.it -------------------------------------------------------- From chemistry-request@server.ccl.net Fri Feb 23 15:19:52 2001 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1NKJqw03237 for ; Fri, 23 Feb 2001 15:19:52 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id OAA11465 for ; Fri, 23 Feb 2001 14:19:58 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.3+Sun/8.9.1) with ESMTP id OAA03002 for ; Fri, 23 Feb 2001 14:19:58 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Fri, 23 Feb 2001 14:19:58 -0600 (CST) From: Jim Phillips To: chemistry@ccl.net Subject: NAMD 2.3b1 Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, NAMD is a free CHARMM and X-PLOR compatible parallel MD code. See http://www.ks.uiuc.edu/Research/namd/ for more information. -Jim +--------------------------------------------------------------------+ | | | NAMD 2.3b1 Release Announcement | | | +--------------------------------------------------------------------+ February 23, 2001 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.3b1 has several advantages over NAMD 2.2: - The new psfgen tool for building PSF structure files. - Simpler to run on a single workstation. (No more rsh!) - New ports to the Compaq AlphaServer SC and Scyld Beowulf. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Fri Feb 23 12:38:36 2001 Received: from drew.berry.edu (drew.berry.edu [66.20.28.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1NHcaw02313 for ; Fri, 23 Feb 2001 12:38:36 -0500 Received: from fsgw.berry.edu (fsgw [66.20.28.25]) by drew.berry.edu (8.9.3/8.9.3) with SMTP id MAA20454 for ; Fri, 23 Feb 2001 12:38:00 -0500 Received: from [10.0.233.81] ([66.20.28.21]) by fsgw.berry.edu; Fri, 23 Feb 2001 12:41:22 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Fri, 23 Feb 2001 12:37:53 -0500 Subject: Question concerning Spartan molecular modeling software From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hello folks, I hope at least some of you have some experience with PC Spartan Pro. I recently purchased several copies of the software and began testing it with some routine molecular mechanics (MMFF94) calculations. Amazingly, when I computed the energy of chlorocyclohexane with the Chlorine in the equatorial position ( 1.4 kcal/mol) it was of HIGHER energy than when the Cl was axial (1.1 kcal/mol). This is contrary to experiment. I ran the same calculation utilizing CambridgeSoft's Chem3D, with Hyperchem (MM+), and MOLGEN (MM2) and received the proper result (i.e., Cl prefers to be equatorial in the chair conformation) and the calculated energy differences were consistent with the experimental values. Has anyone else observed this? is it a result of the force field? Am I doing something wrong in Spartan that I am NOT doing in the other packages? If it is the force field, can I replace the parameters contained within Spartan? Thanks for your help! Gary W. Breton Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 From chemistry-request@server.ccl.net Fri Feb 23 13:59:34 2001 Received: from garaged.fis.unam.mx (IDENT:root@[132.248.33.226]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1NIxXw02607 for ; Fri, 23 Feb 2001 13:59:34 -0500 Received: from yahoo.com (IDENT:max@localhost [127.0.0.1]) by garaged.fis.unam.mx (8.9.3/8.9.3) with ESMTP id NAA23079 for ; Fri, 23 Feb 2001 13:03:03 -0600 Sender: max@garaged.fis.unam.mx Message-ID: <3A96B3E7.97D941F0@yahoo.com> Date: Fri, 23 Feb 2001 13:03:03 -0600 From: Max Organization: UAEM X-Mailer: Mozilla 4.72 [es] (X11; U; Linux 2.2.14-5.0smp i686) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: "Big"jobs on QC in RH6.2 plataform - kernel ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers Thanks for the replys, I have a lot of new info about the problem, I will summarize answers in short. It may be a Kernel problem for what Doug Fox said. I will try it and send back my experience. But there is a problem, i cannot find 2.2.14-12smp, I only found kernel 2.2.16 - 22smp. If anybody knows where i can find it, I only look for it in redhat webpage, I don't know where else I can search. Thank you all!, I really apreciate your interest. I have my suscription to CCL now, but any personal comment or anything can be sent to maxvaldez@yahoo.com again :-) Max -- BE CAREFUL NOT TO BECOME TOO GOOD OF A SONGBIRD OR THEY'LL THROW YOU INTO A CAGE. -- SNOOPY TO WOODSTOCK From chemistry-request@server.ccl.net Fri Feb 23 18:00:20 2001 Received: from web614.mail.yahoo.com (web614.mail.yahoo.com [216.115.104.83]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1NN0Kw04380 for ; Fri, 23 Feb 2001 18:00:20 -0500 Message-ID: <20010223230026.18140.qmail@web614.mail.yahoo.com> Received: from [130.63.75.20] by web614.mail.yahoo.com; Fri, 23 Feb 2001 15:00:26 PST Date: Fri, 23 Feb 2001 15:00:26 -0800 (PST) From: Tim Guo Subject: DFT stabilty, spin containation, and freq. with G98. To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL'ers, I am using DFTs (B3LYP and BP86) in G98 to do some calculations on sc-containing molecules/ions. I would like to get your helps to solve following problems: 1. For some species, the wavefunctions are unstable. When I used "Stable=opt" to reoptimize the wf, I found sometimes the job was aborted because the search did not lower the energy significantly. (e.g. for ScH+, the B3LYP wf can be reoptimized, but BP86 wf reoptimization was aborted.) Do you have special techniques to deal with this kind problem? 2. Sometimes the Stable=opt works well for some species with unstable wavefunctions. It can gave a lower energy, but the spin containation becomes even higher than the unstable wf. What's the problem? 3. When I calculate frequency in compound job step after the stable=opt with guess=read and geom=checkpoint, I find the calculation still uses the unstable wf and gives athe higher energy in the output. What's the right way to calculate frequency by using the reoptimized wf? Thanks a lot in advance! I am looking forward to your replies. Best regards, Tim Guo Email: timguo99@yahoo.com __________________________________________________ Do You Yahoo!? Yahoo! Auctions - Buy the things you want at great prices! http://auctions.yahoo.com/