From owner-chemistry@ccl.net Fri Feb 13 03:42:01 2009 From: "xunlei ding dingxunlei#%#gmail.com" To: CCL Subject: CCL:G: G- Stop at L103 Message-Id: <-38602-090213033404-30600-qDuag5A6UJPG0xB/iFt0aA*_*server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 13 Feb 2009 16:33:50 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei###gmail.com] Dear CCLers, Sometimes the G03 jobs halt at L103 and the last two lines of the output file are " GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad" and "Berny optimization.". The jobs will not stop unless I kill them. Does anybody know how to solve this problem? Best regards, Ding From owner-chemistry@ccl.net Fri Feb 13 04:27:00 2009 From: "xunlei ding dingxunlei::gmail.com" To: CCL Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? Message-Id: <-38603-090213034153-31179-CGPFO8wZmGzeJLkDWbCDdg::server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 13 Feb 2009 16:41:43 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei.:.gmail.com] Dear CCLers, In the manual of G03, the key word "SCF= Symm" is discribed as below: Retain all symmetry constraints: make the number of occupied orbitals of each symmetry type (abelian irreducible representation) match that of the initial guess. Use this option to retain a specific state of the wavefunction throughout the calculation. It is the default only for GVB calculations. But sometimes it doesn't work and the last state is different from the initial state. Could you give me more suggestions on how to retain the symmetry in a SCF calculation? Thanks! Best regards, Ding From owner-chemistry@ccl.net Fri Feb 13 06:20:01 2009 From: "Rajagopalan S. r.subramanian- -ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: G- Stop at L103 Message-Id: <-38604-090213055958-28062-rIiCCnFuDsqIIdIWZd4AHQ-,-server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Feb 2009 11:22:02 +0100 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian]^[ipc.uni-stuttgart.de] Hi, i think you have to increase your computation time..how big is your molecule? how much time did you already used for calculation? xunlei ding dingxunlei#%#gmail.com wrote: > Sent to CCL by: xunlei ding [dingxunlei###gmail.com] > Dear CCLers, > > Sometimes the G03 jobs halt at L103 and the last two lines of the > output file are > " GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad" > and "Berny optimization.". > The jobs will not stop unless I kill them. > Does anybody know how to solve this problem? > > Best regards, > Ding> > > From owner-chemistry@ccl.net Fri Feb 13 06:54:01 2009 From: "Sangeetha Vimal srdshigella-x-gmail.com" To: CCL Subject: CCL: Chemical library analysis tool Message-Id: <-38605-090213062522-31536-spEmAiqgtJVba1dx0Sw6tg#,#server.ccl.net> X-Original-From: "Sangeetha Vimal" Date: Fri, 13 Feb 2009 06:25:18 -0500 Sent to CCL by: "Sangeetha Vimal" [srdshigella,gmail.com] Hi all, Can someone suggest me a chemical library analysis tool, which can help in clustering/diversity analysis of chemical compounds in the database. Thanks Sangeetha From owner-chemistry@ccl.net Fri Feb 13 08:12:00 2009 From: "Radoslaw Kaminski rkaminski.rk!A!gmail.com" To: CCL Subject: CCL: AIM2000 and integration of atomic basins Message-Id: <-38606-090213080655-21318-YdLAKeclsz81pc6UEe4i3A(a)server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Fri, 13 Feb 2009 08:06:50 -0500 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]-[gmail.com] Hello Everyone, I have calculated the electronic structure of some organic molecules having oxygen or sulphur, the total number of non-hydrogen atoms is about 20-25, with B3LYP/6-311++G**. After obtaining the WFN file and doing the integration (in AIM2000 program) of all atoms the sum of AIM charges is about 1.3 e... Is it OK or not? I think that is quite big value. All atoms were integrated well (the integrated Laplacian was good). Can somebody comment on it or help me with improving the method? It is connected with the stability of wave function? All the best Radek Kaminski From owner-chemistry@ccl.net Fri Feb 13 08:46:00 2009 From: "Michel Petitjean petitjean.chiral*gmail.com" To: CCL Subject: CCL: Chemical library analysis tool Message-Id: <-38607-090213080831-21455-aDxnxl3b7JrQXOPiDPyawA[#]server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 13 Feb 2009 14:08:20 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral{}gmail.com] Hi Sangeetha, You did not specify if you need to address 2D or 3D libraries. Anyway, please look at the MCG freeware on my web page: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html MCG produce clusters on the basis of a dissimilarity array (or from numerical variables): you just have to generate these dissimilarities or distances (non necessarily euclidean) between compounds, so that it reflects what you need. The algorithm is O(N^3), N being the number of compounds. Best regards, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean*o*cea.fr, petitjean.chiral*o*gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html ....................................................................................................................... Sent to CCL by: "Sangeetha Vimal" [srdshigella,gmail.com] Hi all, Can someone suggest me a chemical library analysis tool, which can help in clustering/diversity analysis of chemical compounds in the database. Thanks Sangeetha From owner-chemistry@ccl.net Fri Feb 13 09:21:01 2009 From: "Vincent Leroux vincent.leroux_._loria.fr" To: CCL Subject: CCL: Chemical library analysis tool Message-Id: <-38608-090213082314-26455-d3jRwebDKMPwr3DYJMgDWQ() server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Feb 2009 14:22:54 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux|a|loria.fr] Hi Sangeetha, These two papers describe interesting programs being developed by academics : http://dx.doi.org/10.1021/ci7001507 (ParaSurf/ParaFit) http://dx.doi.org/10.1007/s11030-006-9033-5 (ScreeningAssistant) The representations of molecules being used are completely different (property-mapped spherical harmonics surfaces of conformers and short descriptors fingerprints respectively), so results of the two programs might be complementary. For clustering I'd rather use the ParaFit, and for quick diversity assessment ScreeningAssistant. If you want to build subsets from large databases for virtual screening, then ParaSurf/ParaFit is fine if you want to select candidates for optimization by selecting the database molecules most 3D-structurally similar to known hits, or at least if you have prior SAR knowledge that allows you to select the most interesting molecular clusters for examination first. If this is not the case, then you might just want to build the most diverse database drug-like subset of a given (much lower) size. ScreeningAssistant is perfectly good for this, see http://dx.doi.org/10.1007/s00894-007-0257-9 Do not hesitate to contact the corresponding authors for more information. VL Sangeetha Vimal srdshigella-x-gmail.com a écrit : > Sent to CCL by: "Sangeetha Vimal" [srdshigella,gmail.com] > Hi all, > > Can someone suggest me a chemical library analysis tool, which can help in clustering/diversity analysis of chemical compounds in the database. > > Thanks > Sangeetha > > From owner-chemistry@ccl.net Fri Feb 13 09:56:00 2009 From: "Do Quoc-Tuan quoctuan.do-$-greenpharma.com" To: CCL Subject: CCL: Chemical library analysis tool Message-Id: <-38609-090213083435-32645-rsXCkBOPUxEanamp/pezqA%a%server.ccl.net> X-Original-From: Do Quoc-Tuan Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Feb 2009 14:34:38 +0100 MIME-Version: 1.0 Sent to CCL by: Do Quoc-Tuan [quoctuan.do---greenpharma.com] Hi Sangeetha, Have a look at ScreenAssistant: http://www.univ-orleans.fr/icoa/screeningassistant/ Best regards, -- Quoc-Tuan ============================================ Greenpharma S.A. 3, Allée du Titane 45100 Orléans FRANCE Tél : +33.2.38.25.99.80 Fax : +33.2.38.25.99.65 mail: quoctuan.do()greenpharma.com web : http://www.greenpharma.com ============================================ Le contenu de ce message et de toute piece jointe est confidentiel et est adresse exclusivement au(x) destinaire(s). Si vous recevez ce message par erreur, veuillez le detruire et informer immediatement l'expediteur. Greenpharma ne peut etre tenu responsable des erreurs de transmission inherant aux courriels, a l'interception et aux modifications frauduleuses du contenu du message et de ses pieces jointes. Greenpharma a pris les précautions raisonnables contre les logiciels malveillants. Par consequent, Greenpharma decline toute responsabilite quant a un eventuel dommage ou contamination de votre systeme informatique. The content of this message and any attachment is confidential and is exclusively intended to its recipient(s). If you receive this e-mail by error, please delete it and notify its sender immediately. Greenpharma is not liable for any transmission errors due to e-mail, any deceptive interception and modification of the content of this message and of its attachment(s). Greenpharma has taken reasonable measures against malware. Therefore, Greenpharma is not liable for any damage or contamination of your information system. From owner-chemistry@ccl.net Fri Feb 13 10:40:01 2009 From: "Johannes Hachmann jh388[*]cornell.edu" To: CCL Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? Message-Id: <-38610-090213090426-21813-IswKAodyLVcrj0lj7gdZkg/a\server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Feb 2009 09:03:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388!A!cornell.edu] Hi Ding, use SCF=QC (however quadratically convergent SCF is a bit costy...). See description under http://www.gaussian.com/g_ur/k_guess.htm on the bottom together with GUESS=ALTER. This is not a particularly elegant way to do things (compared to just specifying the state symmetry in e.g. MOLPRO) but it works. You might want to use the STABLE option so that you know whether you have instabilities to which other states and which additional MO swaps you might want to perform. Best Johannes --------------------------------------------------------------- Johannes Hachmann (Dipl.-Chem., M.Sc.) Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu,,ccl.net > [mailto:owner-chemistry+jh388==cornell.edu,,ccl.net] On Behalf > Of xunlei ding dingxunlei::gmail.com > Sent: Friday, February 13, 2009 3:42 AM > To: Hachmann, Johannes > Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? > > > Sent to CCL by: xunlei ding [dingxunlei.:.gmail.com] Dear CCLers, > > In the manual of G03, the key word "SCF= Symm" is discribed as below: > Retain all symmetry constraints: make the number of occupied > orbitals of each symmetry type (abelian irreducible > representation) match that of the initial guess. Use this > option to retain a specific state of the wavefunction > throughout the calculation. It is the default only for GVB > calculations. > > But sometimes it doesn't work and the last state is different > from the initial state. > > Could you give me more suggestions on how to retain the > symmetry in a SCF calculation? > > Thanks! > > Best regards, > Ding > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the ,, sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > From owner-chemistry@ccl.net Fri Feb 13 11:17:00 2009 From: "Igor Filippov Contr igorf#%#helix.nih.gov" To: CCL Subject: CCL: Chemical library analysis tool Message-Id: <-38611-090213102643-20187-KdzIrYpOt9ShTJchp6vsRw{}server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 13 Feb 2009 08:55:26 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf-.-helix.nih.gov] Pipeline Pilot http://accelrys.com/products/scitegic/ Cheers, Igor On Fri, 2009-02-13 at 06:25 -0500, Sangeetha Vimal srdshigella-x-gmail.com wrote: > Sent to CCL by: "Sangeetha Vimal" [srdshigella,gmail.com] > Hi all, > > Can someone suggest me a chemical library analysis tool, which can help in clustering/diversity analysis of chemical compounds in the database. > > Thanks > Sangeetha> -- Igor Filippov [Contr] From owner-chemistry@ccl.net Fri Feb 13 17:06:01 2009 From: "Roman D Gorbunov rgorbuno^_^aecom.yu.edu" To: CCL Subject: CCL:G: Hessian matrix in Cartesian coordinates by Gaussian. Message-Id: <-38612-090213170249-14902-U+SVJjY7jCqa4B1UKx5tBw:-:server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Fri, 13 Feb 2009 17:02:45 -0500 Sent to CCL by: "Roman D Gorbunov" [rgorbuno(0)aecom.yu.edu] Dear CCL Subscribers, I need to calculate the Hessian matrix in Cartesian coordinates. I searched for the answer in the Interned found this: http://www.ccl.net/chemistry/resources/messages/2005/10/03.007-dir/ It is written that first I have to calculate the checkpoint file. Then I have to use "formchk name.chk name.fchk" to get a formated file. And finally I have to use a script called "demofc" to extract the Hessian matrix given in the Cartesian coordinates. I have a problem with the last step. I do not know how exactly should I use the "demofc". I also cannot find any useful information about that. Could anybody pleas help me with that? By the way, I checked the formated checkpoint file (name.fchk). It contains some information about the system, but I did not find there anything about Hessian matrix. May be I have to put some additional keywords into the Gaussian input file to force Gaussian to calculate the Hessian matrix? Roman From owner-chemistry@ccl.net Fri Feb 13 19:28:01 2009 From: "John Edward jeedward ~~ yahoo.com" To: CCL Subject: CCL: Draft paper submission deadline extended: BCBGC-09 Message-Id: <-38613-090213192708-22856-dM9ws74t6jBB00yOO4sZrQ~!~server.ccl.net> X-Original-From: "John Edward" Date: Fri, 13 Feb 2009 19:27:04 -0500 Sent to CCL by: "John Edward" [jeedward%a%yahoo.com] Draft paper submission deadline extended: BCBGC-09 The deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors. The conference will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) International Conference on Automation, Robotics and Control Systems (ARCS-09) International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) International Conference on Information Security and Privacy (ISP-09) International Conference on Recent Advances in Information Technology and Applications (RAITA-09) International Conference on Software Engineering Theory and Practice (SETP-09) International Conference on Theory and Applications of Computational Science (TACS-09) International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) The website http://www.PromoteResearch.org contains more details. Sincerely John Edward Publicity committee From owner-chemistry@ccl.net Fri Feb 13 20:49:00 2009 From: "Roman D Gorbunov rgorbuno:+:aecom.yu.edu" To: CCL Subject: CCL: Hessian matrix in Cartesian coordinates by Gaussian. Message-Id: <-38614-090213204822-22708-VgvqL1QJO2061lfbZOk+Sg ~~ server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Fri, 13 Feb 2009 20:48:18 -0500 Sent to CCL by: "Roman D Gorbunov" [rgorbuno~~aecom.yu.edu] I think I found the answer on my question. In the formated checkpoint file there is a block called "Cartesian Force Constants". It should be nothing but the Hessian matrix in the Cartesian coordinates.