From chemistry-request@ccl.net Tue Nov 11 18:58:01 2003 Received: from smtp2.server.rpi.edu (smtp2.server.rpi.edu [128.113.2.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hABNvU9c019775 for ; Tue, 11 Nov 2003 18:57:30 -0500 Received: from rpi.edu (omniocular-42.dynamic.rpi.edu [128.113.135.51]) by smtp2.server.rpi.edu (8.12.10/8.12.9) with ESMTP id hABNvSXE025964; Tue, 11 Nov 2003 18:57:28 -0500 Message-ID: <3FB17774.6B1C0959^at^rpi.edu> Date: Tue, 11 Nov 2003 18:57:40 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry^at^ccl.net, qsar_society^at^accelrys.com Subject: Announcement - ACS COMP Division CCG Excellence Award Winners - Anaheim 2004. Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Computational Chemistry Community, On behalf of the ACS Division of Computers in Chemistry and the Chemical Computing Group, it is my pleasure to announce the winners of the CCG Excellence Award for the 227th ACS National Meeting in Anaheim, California. All of the applications received were of the highest quality, and the panel of judges had to make many tough choices. Those not selected for Awards this time are encouraged to reapply for the Philadelphia meeting. The winners have earned up to $1,150 in expense reimbursements to cover their travel and local expenses during the meeting. They will also be honored during a ceremony at the COMP Division Poster Session and then attend an Awardee Dinner on Tuesday evening, March 30th. Each winner will also receive a one year license to the most current MOE software for their research group. Congratulations to the winners! They are listed here in no particular order: Xiaolin Cheng - "Molecular Dynamics Simulations of 8-oxoguanine:A mismatch DNA" Department of Chemistry and Center for Structural Biology, Stony Brook University Alexander Perryman - "HIV-1 Protease Molecular Dynamics of a Wild-Type and of the V82F/I84V Mutant: Possible Contributions to Drug Resistance and a Potential New Target Site for Drugs." Howard Hughes Medical Institute, Department of Pharmacology, & Dept. of Chemistry and Biochemistry*, University of California at San Diego, La Jolla, CA 92093-0365 Asif Ladiwala - "Prediction of Protein Affinity in Hydrophobic Interaction Chromatography using Quantitative Structure-Retention Relationship (QSRR) Models". Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180 Asim Okur - "Multiple pathways in beta-hairpin folding and unfolding simulations". Department of Chemistry, Stony Brook University Jessica Swanson - "Revisiting Free Energy Calculations: One Step Closer to Rigorous Scoring Functions and One Step beyond MM/PBSA". Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0365 Ivan Tubert-Brohman - "Improved Semiempirical Methods: Parameterization of PDDG/PM3 for Sulfur" Yale University, Department of Chemistry P.O. Box 208107, New Haven, CT 06520-8107. Sarah A. Mueller Stein - "The Influence of Steric Congestion on the Dynamics and Geometry of DNA". Duquesne University, 308 Mellon Hall, 600 Forbes Avenue, Pittsburgh, PA 15282. Wei (David) Deng - "Predicting Protein-Ligand Binding Affinities using Transferable Atom Equivalent (TAE) Techniques And Machine-Learning Methods". Department of Chemistry, Rensselaer Polytechnic Institute, Troy, NY 12180 Andreas Bender - "Similarity Searching using Atom Environments, Information Gain based Feature Selection and the Naove Bayesian Classifier" Unilever Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom Anne E. Loccisano - "Development of New CHARMM Force Field Parameters for Novel DNA Bending Agents" Duquesne University, 308 Mellon Hall, 600 Forbes Avenue, Pittsburgh, PA 15282. ================ We applaud all of the applicants, and encourage graduate students working in the field of Computational Chemistry to apply for the next round of CCG Excellence Awards for the Philadelphia ACS National Meeting, August 22-26, 2004 Please watch your E-mail for announcements of the next deadline for submission of application packages for COMP's CCG Excellence Award! Curt M. Breneman COMP Division Treasurer Professor of Chemistry RPI 110 8th St Troy, NY 12180 From chemistry-request@ccl.net Tue Nov 11 11:17:31 2003 Received: from web15203.mail.bjs.yahoo.com (web15203.mail.cnb.yahoo.com [202.3.77.133]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hABGGx9c010255 for ; Tue, 11 Nov 2003 11:16:59 -0500 Message-ID: <20031111161657.42596.qmail^at^web15203.mail.bjs.yahoo.com> Received: from [211.138.102.93] by web15203.mail.bjs.yahoo.com via HTTP; Wed, 12 Nov 2003 00:16:57 CST Date: Wed, 12 Nov 2003 00:16:57 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: How to display protein in Sybyl To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.1 required=7.0 tests=DATE_IN_PAST_12_24 version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I have a question with displaying the protein molecule in sybyl 6.7. The sybyl 6.7 could read protein structure in pdb format, however, it can not display the protein on screen, even the ligand. Does it need any special setting? Any suggestions will be very appreciated. Thanks in advance. Regards, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong^at^yahoo.com.cn __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Tue Nov 11 17:53:54 2003 Received: from mail.uni-kl.de (mail.uni-kl.de [131.246.137.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hABMrM9c018551 for ; Tue, 11 Nov 2003 17:53:23 -0500 Received: from mailgate1.uni-kl.de (mailgate1.uni-kl.de [131.246.120.5]) by mail.uni-kl.de (8.12.8/8.12.8) with ESMTP id hABMrMrk024704 for ; Tue, 11 Nov 2003 23:53:22 +0100 (MET) Received: from service.chemie.uni-kl.de (service.chemie.uni-kl.de [131.246.58.77]) by mailgate1.uni-kl.de (8.12.10/8.12.10) with ESMTP id hABMrLQo006770 for ; Tue, 11 Nov 2003 23:53:22 +0100 Received: from pc1.chemie.uni-kl.de (pc1.chemie.uni-kl.de [131.246.58.1]) by service.chemie.uni-kl.de (Postfix) with ESMTP id A655D36D02 for ; Wed, 12 Nov 2003 00:12:56 +0100 (CET) Received: from pc3 (pc3.chemie.uni-kl.de [131.246.58.3]) by pc1.chemie.uni-kl.de (Postfix) with ESMTP id 9ACC713C8D for ; Tue, 11 Nov 2003 23:53:21 +0100 (CET) Content-Type: text/plain; charset="iso-8859-1" From: Elmar Gerwalin Reply-To: elg^at^chemie.uni-kl.de To: chemistry^at^ccl.net Subject: g98: strange DIIS values Date: Tue, 11 Nov 2003 23:53:20 +0100 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200311112353.20710.elg^at^chemie.uni-kl.de> X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL'lers. I have a strange G98 problem: After re-installation of g98 rev a.9, g98 produces different DIIS values, sometimes all are 0.0D+00 and thus in these cases no SCF- convergence is reached. Major differences in the DIIS values compared to other systems (e.g. i386) exist: < DIIS: error= 2.82D-01 at cycle 1. < DIIS: error= 1.68D-02 at cycle 2. < DIIS: error= 2.33D-02 at cycle 3. --- > DIIS: error= 5.44D+00 at cycle 1. > DIIS: error= 6.89D-01 at cycle 2. > DIIS: error= 1.26D+00 at cycle 3. Energies are only slightly different: < Version=DEC-AXP-Linux-G98RevA.9 Version=DEC-AXP-Linux-G98RevA.9 --- > Version=x86-Linux-G98RevA.9 45,47c45,47 < HF=-350.5663313 < RMSD=4.195e-05 < Dipole=0.1266355,-0.256456,0. --- > HF=-350.5663311 > RMSD=2.964e-05 > Dipole=0.1278141,-0.2582534,0. --- > Version=x86-Linux-G98RevA.9 45,47c45,47 < HF=-350.5663313 < RMSD=4.195e-05 < Dipole=0.1266355,-0.256456,0. --- > HF=-350.5663311 > RMSD=2.964e-05 > Dipole=0.1278141,-0.2582534,0. I would expect very little differences compared to other hardware systems, but even differences to jobs that were run on the same machine some time ago exist ! I didn't change the OS and the hardware. The system : DEC Alpha, 64 bit, Debian Linux Gaussian 98: DEC-AXP-Linux-G98RevA.9 19-Apr-2000 Did someone have the same experiences and is able to help me ? Yours, Elmar ======================================================== Elmar Gerwalin , University of Kaiserslautern,Germany Dept. of Theoretical Chemistry and IT Service Team elg^at^chemie.uni-kl.de 0631-205-2749 ======================================================== From chemistry-request@ccl.net Tue Nov 11 10:14:47 2003 Received: from mercury.chem.pitt.edu (mercury.chem.pitt.edu [136.142.60.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hABFEE9c008732 for ; Tue, 11 Nov 2003 10:14:14 -0500 Received: from ringo.chem.pitt.edu (localhost.localdomain [127.0.0.1]) by mercury.chem.pitt.edu (Postfix) with SMTP id BC09F483D for ; Tue, 11 Nov 2003 10:12:38 -0500 (EST) Received: from 150.161.200.40 (SquirrelMail authenticated user gustavo) by mercury.chem.pitt.edu with HTTP; Tue, 11 Nov 2003 10:12:38 -0500 (EST) Message-ID: <33321.150.161.200.40.1068563558.squirrel)at(mercury.chem.pitt.edu> Date: Tue, 11 Nov 2003 10:12:38 -0500 (EST) Subject: Sum Over States with damping From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL readers, I am interested in doing Sum Over States calculations of absorption of two photons. I have read several papers including the paper by Orr and Ward in Molecular Physics 20, 513 (1971). When comparing equation 43c from Orr and Ward with the equation in more recent papers that cite Orr and Ward, I found different signs in front of the damping factors (they are all negative). My question is: can anyone explain the discrepancy in these signs? Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura gustavo)at(mercury.chem.pitt.edu From chemistry-request@ccl.net Tue Nov 11 10:09:08 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hABF8a9c008510 for ; Tue, 11 Nov 2003 10:08:37 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HO7006CI0Q9FW)at(mailserver.unimi.it> for chemistry)at(ccl.net; Tue, 11 Nov 2003 16:08:35 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HO700H1S0Q7HR)at(smtp.unimi.it> for chemistry)at(ccl.net; Tue, 11 Nov 2003 16:08:31 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id CD20C320AD; Tue, 11 Nov 2003 16:20:43 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id A1E4D2F34D for ; Tue, 11 Nov 2003 16:20:43 +0100 (CET) Date: Tue, 11 Nov 2003 16:20:42 +0100 (CET) From: Alessandro Contini Subject: converting .cif files To: chemistry)at(ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hABF989c008523 Hi, does anybody knows any free software for converting .cif crystallographic data files into standard visualization formats (xyz, pdb, mol2, etc.)? Thanks a lot Alessandro Contini Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini)at(unimi.it From chemistry-request@ccl.net Tue Nov 11 15:33:12 2003 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hABKWe9c015726 for ; Tue, 11 Nov 2003 15:32:41 -0500 Received: by lgdx04.lg.ehu.es id VAA0000014774; Tue, 11 Nov 2003 21:32:40 +0100 (MET) Message-ID: <005c01c3a88a$93323440$222fe39e!at!lc.ehu.es> From: "Pablo Vitoria" To: "CCL" Subject: Gaussian03 Binary vs. Source Date: Tue, 11 Nov 2003 20:32:41 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0059_01C3A892.F4A2AFE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.0 required=7.0 tests=HTML_30_40,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0059_01C3A892.F4A2AFE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I am about to buy Gaussian03 to run it on Linux. I wanted to buy the = source in order to optimize it for each processor (I have both Athlon = and Xeon machines), but Gaussian only supports PGF77 compiler. I wonder = if someone out there could share sone information about: - Is it possible to use g77 or Intel ifc to compile g03? Any success? - Will the I suffer a significant performance penalty if I buy the = Athlon (PII or higher) binary to run it also on the Xeons (in order to = save money:-) ? - Any problems with Mandrake, instead of the supported Red Hat and Suse? Thank you very much Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qu=EDmica Inorg=E1nica, Facultad de Ciencias Universidad del Pa=EDs Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6015992 Fax. 94 4648500 ------=_NextPart_000_0059_01C3A892.F4A2AFE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
Hi all,
 
I am about to buy Gaussian03 to run it = on Linux. I=20 wanted to buy the source in order to optimize it for each processor (I = have both=20 Athlon and Xeon machines), but Gaussian only supports PGF77 compiler. I = wonder=20 if someone out there could share sone information about:
 
- Is it possible to use g77 or Intel = ifc to compile=20 g03? Any success?
- Will the I suffer a significant = performance=20 penalty if I buy the Athlon (PII or higher) binary to run it also on the = Xeons=20 (in order to save money:-) ?
- Any problems with Mandrake, instead = of the=20 supported Red Hat and Suse?
 
Thank you very much
 
Pablo
--------------------------------------------------------
Pabl= o Vitoria=20 Garcia
Dpto. Qu=EDmica Inorg=E1nica, Facultad de = Ciencias
Universidad del Pa=EDs=20 Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)
 
Tfno. 94 6015992
Fax. 94=20 4648500
------=_NextPart_000_0059_01C3A892.F4A2AFE0-- From chemistry-request@ccl.net Tue Nov 11 07:01:41 2003 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hABC169c003141 for ; Tue, 11 Nov 2003 07:01:09 -0500 Received: by lgdx04.lg.ehu.es id NAA0000006623; Tue, 11 Nov 2003 13:01:01 +0100 (MET) Message-ID: <000a01c3a84b$7d01f640$222fe39e!at!lc.ehu.es> From: "Pablo Vitoria" To: "CCL" Subject: Gaussian03 Binary vs. Source Date: Tue, 11 Nov 2003 13:01:06 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C3A853.DE84C160" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=1.0 required=7.0 tests=HTML_30_40,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C3A853.DE84C160 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I am about to buy Gaussian03 to run it on Linux. I wanted to buy the = source in order to optimize it for each processor (I have both Athlon = and Xeon machines), but Gaussian only supports PGF77 compiler. I wonder = if someone out there could share sone information about: - Is it possible to use g77 or Intel ifc to compile g03? Any success? - Will the I suffer a significant performance penalty if I buy the = Athlon (PII or higher) binary to run it also on the Xeons (in order to = save money:-) ? - Any problems with Mandrake, instead of the supported Red Hat and Suse? Thank you very much Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qu=EDmica Inorg=E1nica, Facultad de Ciencias Universidad del Pa=EDs Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6015992 Fax. 94 4648500 ------=_NextPart_000_0007_01C3A853.DE84C160 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
I am about to buy Gaussian03 to run it = on Linux. I=20 wanted to buy the source in order to optimize it for each processor (I = have both=20 Athlon and Xeon machines), but Gaussian only supports PGF77 compiler. I = wonder=20 if someone out there could share sone information about:
 
- Is it possible to use g77 or Intel = ifc to compile=20 g03? Any success?
- Will the I suffer a significant = performance=20 penalty if I buy the Athlon (PII or higher) binary to run it also on the = Xeons=20 (in order to save money:-) ?
- Any problems with Mandrake, instead = of the=20 supported Red Hat and Suse?
 
Thank you very much
 
Pablo
--------------------------------------------------------
Pabl= o Vitoria=20 Garcia
Dpto. Qu=EDmica Inorg=E1nica, Facultad de = Ciencias
Universidad del Pa=EDs=20 Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)
 
Tfno. 94 6015992
Fax. 94=20 4648500
------=_NextPart_000_0007_01C3A853.DE84C160-- From chemistry-request@ccl.net Wed Nov 12 05:14:05 2003 Received: from jeeves.ccdc.cam.ac.uk (jeeves.ccdc.cam.ac.uk [131.111.113.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hACADX9c001202 for >ccl.net>; Wed, 12 Nov 2003 05:13:33 -0500 Received: from sun14.ccdc.cam.ac.uk ([131.111.113.48] helo=ccdc.cam.ac.uk) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 3.35 #1 (CCDC Mailserver)) id 1AJs0B-0007Kf-00; Wed, 12 Nov 2003 10:13:31 +0000 Message-ID: <3FB207CA.7B2C0518<>ccdc.cam.ac.uk> Date: Wed, 12 Nov 2003 10:13:30 +0000 From: Jacco van de Streek >ccdc.cam.ac.uk> Organization: CCDC X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: Alessandro Contini >unimi.it> CC: chemistry<>ccl.net Subject: Re: CCL:converting .cif files References: >heisenberg.chimica.unimi.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-CCDC-MailScanner: Not scanned: please contact syseng for details. X-CCDC-SpamCheck: X-Spam-Status: No, hits=-2.1 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Alessandro Contini wrote: > does anybody knows any free software for converting .cif crystallographic > data files into standard visualization formats (xyz, pdb, mol2, etc.)? Mercury can do this: http://www.ccdc.cam.ac.uk/prods/mercury/index.html It can be downloaded for free and for a variety of platforms. Best wishes, -- Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge, United Kingdom From chemistry-request@ccl.net Wed Nov 12 08:36:27 2003 Received: from nankai.edu.cn (sun.nankai.edu.cn [202.113.16.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hACDZr9c007145 for ; Wed, 12 Nov 2003 08:35:55 -0500 Message-Id: <200311121335.hACDZr9c007145$at$server.ccl.net> Received: (eyou send program); Wed, 12 Nov 2003 21:36:43 +0800 Received: from 202.113.231.116 by 202.113.16.21 with HTTP; Wed, 12 Nov 2003 21:36:43 +0800 X-WebMAIL-MUA: [202.113.231.116] From: "T,>2" To: chemistry$at$ccl.net Date: Wed, 12 Nov 2003 21:36:43 +0800 Reply-To: "T,>2" Subject: Some question in using Tinker Content-Type: text/plain X-Spam-Status: No, hits=3.8 required=7.0 tests=DEAR_SOMETHING,HEADER_8BITS version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Sir or madam: I meet some difficulties in making a chloroform (CHCl3) box in NPT conditions byusing tinker. In NPT simulation(300K,1atm),the density is about 1.30g/ml,which is smaller than experimental data(1.48g/ml), and the delta H(vap) didn't agree to experimental data. Could you give me some advice on how to make the box more reseanable?I want to use "rattle bonds" keyword to control the bond length as 1.758A, however, there is errors as "constrain not satisfatied".Could you tell me where is wrong ? My tinker.key file is: forcefield OPLS United-ATOM vdwtype LENNARD-JONES radiusrule GEOMETRIC radiustype SIGMA radiussize DIAMETER epsilonrule GEOMETRIC torsionunit 0.5 vdw-14-scale 0.5 chg-14-scale 0.5 dielectric 1.0 a-axis 30.00 cut-off 14.00 TAU-TEMPERATURE 0.1 rattle bonds integrate verlet atom 1 CH "CHCl3 CH " 7 13.018 3 atom 2 Cl "CHCl3 CH " 17 35.453 1 vdw 1 3.8000 0.0800 vdw 2 3.4700 0.3000 bond 1 2 245.0 1.7580 angle 1 2 3 78.00 110.30 charge 1 0.4200 charge 2 -0.1400 YuanJing Nankai University P.R.China E-mail:yuanjingnk$at$nankai.edu.cn From chemistry-request@ccl.net Wed Nov 12 03:49:55 2003 Received: from relay2.uni-heidelberg.de (relay2.uni-heidelberg.de [129.206.210.211]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hAC8nO9c031620 for ; Wed, 12 Nov 2003 03:49:24 -0500 Received: from ix.urz.uni-heidelberg.de (mail.urz.uni-heidelberg.de [129.206.119.234]) by relay2.uni-heidelberg.de (8.12.10/8.12.10) with ESMTP id hAC8nNsR013688 for ; Wed, 12 Nov 2003 09:49:23 +0100 (MET) Received: from extmail.urz.uni-heidelberg.de (extmail.urz.uni-heidelberg.de [129.206.100.140]) by ix.urz.uni-heidelberg.de (8.8.8/8.8.8) with SMTP id JAA29718 for ; Wed, 12 Nov 2003 09:49:23 +0100 Received: (qmail 11561 invoked by uid 0); 12 Nov 2003 08:49:22 -0000 Received: from unknown (HELO web.de) (unknown) by unknown with RC4-MD5 encrypted SMTP; 12 Nov 2003 08:49:21 -0000 Message-ID: <3FB1F3D9.80405)at(web.de> Date: Wed, 12 Nov 2003 09:48:25 +0100 From: =?ISO-8859-1?Q?Andr=E9_Daubinet?= User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL Subject: CCL: Setting Element Mass in SP Calc Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hallo everyone, I have the following problem: I would like to do a series of SP calculation on a series of Tc compounds in guassian 98/03. When I try and attempt a calculation I get a warning mesg.: atom type 43 mass uknown, setting to 1. IS there anyway I can set the mass for the element ? Many thanx Andre From jkl@ccl.net Wed Nov 12 14:03:00 2003 -0500 Message-ID: <007201c3a943$db6e7ca0$2c03a8c0@espectro> From: "Reynier Suardiaz del Rio" To: Subject: Semiempirical parameters for Ru and Fe? Date: Wed, 12 Nov 2003 13:38:55 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_006F_01C3A922.51902810" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Checker-Version: SpamAssassin 2.60 (1.212-2003-09-23-exp) on atlantis.ccl.net X-Spam-Status: No, hits=1.1 required=9.0 tests=BAYES_44,FORGED_OUTLOOK_TAGS, HTML_MESSAGE autolearn=no version=2.60 This is a multi-part message in MIME format. ------=_NextPart_000_006F_01C3A922.51902810 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Does anybody knows a software with semiempirical parameters of Ru or Fe? =20 Best=20 =20 Reynier =20 Thanks Reynier ------=_NextPart_000_006F_01C3A922.51902810 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Does anybody knows a software with = semiempirical=20 parameters of Ru or Fe?
 
 Best
 =20
Reynier
 
Thanks
Reynier
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