MOPAC 7

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----- Original Messag= e ----
From: Green Power powergreen%a%gmail.com <owner-chemistry:_:ccl.= net>
To: "Wang, Yun " <wangyun22:_:yahoo.com>
Sent: Fr= iday, 24 August, 2007 6:58:26 AM
Subject: CCL: Semi empirical PBC progra= m

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=0ASick of deleting your inbo= x? Yahoo!7 Mail has free unlimited storage. Get it now.=0A --0-607431699-1187915072=:18689-- From owner-chemistry@ccl.net Fri Aug 24 11:29:01 2007 From: "Close, David M. CLOSED{=}mail.etsu.edu" To: CCL Subject: CCL:G: Thermochemical calculations from Gaussian output file Message-Id: <-35013-070824100835-17936-bUOleSw15kDJCSW3uHyDEA[A]server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 24 Aug 2007 10:08:27 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED,mail.etsu.edu] Yangsoo: For the thermodynamic information you must run a FREQ calculation from the normal Gaussian output (from the .chk file). This is describe in the Gaussian Manual. For ionization energy you have to calculate the difference in energy between the ground state and the one electron oxidized state. This involves a separate calculation on the cation. For the electron affinity, you also have to do a separate calculation. Here I would suggest a thorough literature search. Depending on the system you are studying, there a many problems deciding on what bases set and method to use to get reliable electron affinities. Regards, Dave Close. From owner-chemistry@ccl.net Fri Aug 24 12:05:01 2007 From: "Lothar Terfloth lothar.terfloth(~)chemie.uni-erlangen.de" To: CCL Subject: CCL: Open Source 3D coordinate generation tool Message-Id: <-35014-070824105529-20444-mIEgMjoUoCy79UMqIYzFdw]*[server.ccl.net> X-Original-From: Lothar Terfloth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Aug 2007 16:55:19 +0200 MIME-Version: 1.0 Sent to CCL by: Lothar Terfloth [lothar.terfloth\a/chemie.uni-erlangen.de] Dear Rajarshi Guha, thanks for your reply. Concerning tetrahedral chirality it is the notation using the at-sign. The at-character obviously has been changed automagically by the scripts processing the e-mails sent to CCL. The notation using the at-character is briefly explained at http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html#STEREO With best regards, Lothar Terfloth Rajarshi Guha rguha- -indiana.edu wrote: > > Sent to CCL by: Rajarshi Guha [rguha-.-indiana.edu] > > On Aug 22, 2007, at 12:00 PM, Lothar Terfloth > lothar.terfloth|,|chemie.uni-erlangen.de wrote: > >> >> Sent to CCL by: Lothar Terfloth [lothar.terfloth,chemie.uni-erlangen.de] >> >> Dear all, >> >> a) SPE is the central step for the generation of a 'rough' set of 3D >> coordinates in smi23d. >> Following >> >> http://www.wipo.int/pctdb/en/wo.jsp?wo=2004003683&IA=WO2004003683&DISPLAY=STATUS >> >> >> or >> >> http://www.wipo.int/pctdb/en/wo.jsp?wo=2004003683&IA=WO2004003683&DISPLAY=STATUS >> >> >> I would assume that there is a patent on the SPE algorithm and its >> application. Does this affect smi23d? > > I will get more concrete information regarding this in a few days > >> >> b) Obviously smi2sdf does not support stereochemistry, e.g. >> >> butene.smi: >> C\C=C\C E-but-2-ene >> C\C=C/C Z-but-2-ene > > smi2sdf does support E/Z stereochemistry and this was a bug - the latest > fixed version is in SVN and builds for OS X and Linux (Fedora Core 64 > bit) have been updated > >> I tried also cis- and trans-decalin. >> >> decalin.smi: >> [H][C*o**o*]12[C*o**o*](CCCC2)([H])CCCC1 cis-decalin >> [H][C*o**o*]12[C*o*](CCCC2)([H])CCCC1 trans-decalin > > I'm not aware of the use of the '*' token to indicate tetrahedral > chirality. If on the other hand I use the following: > > C1CC[C:-::-:H]2CCCC[C:-:H]2C1 trans-decalin > C1CC[C:-:H]2CCCC[C:-:H]2C1 cis-decalin > > it works fine > >> c) I made a very brief comparision with CORINA on a data set >> of 146 cytochrome P450 substrates which has been published >> recently (http://dx.doi.org/10.1021/ci700010t & suppl. material). > > Thanks for the comparison - we certainly make no claims to speed :) > > We are in the process of generating benchmarks wrt timing and ability to > handle complex molecules. > >> d) How long did it take to generate Pub3D? > > This is a little tricky to answer since we switched between different > machines as well as had to regenerate certain portions of the database > while we got our workflow in place. Overall we took about a month or so, > but this is obviously not a rigorous statement since there was a number > of days of downtime etc. > > As I noted above, we'll be running benchmarks so hopefully in the next > few weeks we'll get a more rigorous answer > >> e) Is mengine based on Pcmodel version 7? ( http://www.serenasoft.com ) > > As with a), I'll get back to you in a few days > > ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > A mathematician is a device for turning coffee into theorems. > -- P. Erdoshttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Fri Aug 24 12:41:01 2007 From: "Joseph M Leonard jleonard42{:}gmail.com" To: CCL Subject: CCL: GRID questions Message-Id: <-35015-070824123650-1224-jlxpyt9Y/CgpJL3xeq66Pw*server.ccl.net> X-Original-From: "Joseph M Leonard" Content-Type: multipart/alternative; boundary="----=_Part_162530_16863145.1187971885719" Date: Fri, 24 Aug 2007 12:11:25 -0400 MIME-Version: 1.0 Sent to CCL by: "Joseph M Leonard" [jleonard42\a/gmail.com] ------=_Part_162530_16863145.1187971885719 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks, it's been a while but I've been rereading the GRID source literature, and I have a few questions I hope CCL readers might know: 1. Is there a published definition of the DRY probe? I recall hearing about this years ago at a conference, but can't remember when. The best I've found so far is a short reference in Curr Med Chem 13,2653(2006), which describes the probe in a sentence or two. 2. Goodford's J Med Chem 28,849(1985) describes the energy functions in terms of older references (which is not unexpected). However, one of them is a book by Hopfinger, published in '73... Does anybody have either the section that describes how the L-J A and B terms are determined, or a copy of the terms corresponding to this paper? 3. Also in JMC 28 is a mention of K in equation 3. I think this comes from the CHARMM reference cited (#11), and I'm pursuing that. If anybody has this on-line I'd appreciate learning its value... Thanks in advance! I worry that Google's effort in scanning books will take a while to get to "old chemical literature" :-). Joe jleonard42++gmail.com ------=_Part_162530_16863145.1187971885719 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks, it's been a while but I've been rereading the GRID source literature, and I have a few questions I hope CCL readers might know:

1. Is there a published definition of the DRY probe? I recall hearing about this years ago at a conference, but can't remember when. The best I've found so far is a short reference in Curr Med Chem 13,2653(2006), which describes the probe in a sentence or two.

2. Goodford's J Med Chem 28,849(1985) describes the energy functions in terms of older references (which is not unexpected). However, one of them is a book by Hopfinger, published in '73... Does anybody have either the section that describes how the L-J A and B terms are determined, or a copy of the terms corresponding to this paper?

3. Also in JMC 28 is a mention of K in equation 3. I think this comes from the CHARMM reference cited (#11), and I'm pursuing that. If anybody has this on-line I'd appreciate learning its value...

Thanks in advance! I worry that Google's effort in scanning books will take a while to get to "old chemical literature" :-).

Joe
jleonard42++gmail.com
------=_Part_162530_16863145.1187971885719-- From owner-chemistry@ccl.net Fri Aug 24 13:49:01 2007 From: "Debellis Anthony CE US anthony.debellis^_^cibasc.com" To: CCL Subject: CCL:G: Thermochemical calculations from Gaussian output file Message-Id: <-35016-070824134427-9583-qg7wiMGDx65Y0TFj817OWw^server.ccl.net> X-Original-From: "Debellis Anthony CE US" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 24 Aug 2007 11:24:30 -0400 MIME-Version: 1.0 Sent to CCL by: "Debellis Anthony CE US" [anthony.debellis|cibasc.com] You might want to have a look at the white paper from Gaussian, Inc. entitled "Thermochemistry in Gaussian". I'm sure it's available on their website. Anthony DeBellis Ciba -----Original Message----- > From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net] Sent: Friday, August 24, 2007 1:25 AM To: Debellis Anthony CE US Subject: CCL:G: Thermochemical calculations from Gaussian output file Sent to CCL by: "Yangsoo Kim" [vsmember-x-gmail.com] Dear all, Im wondering if anyone of you performed the thermochemical calculations > from Gaussian output. What wed like to do is to calculate heat of formation, ionization energy, electron affinity, proton affinity, and bond dissociation energy from Gaussian output files. We first tried to perform those calculations based on some published approaches (e.g., Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds, L. A. Curtiss, P. C. Redfern, and D. J. Frurip, Reviews of Computational Chemistry, Volume 15 Edited by K. B. Lipkowitz and D. B. Boyd pp.147-202). Unfortunately, our calculation results do not match the data that have been available in the computational thermochemistry literature. I'd appreciate if anyone can suggest how to get those thermochmical property values out of Gaussian output file. Due to our tight project schedule, it would be the best if any commercial or open (free) code or software is available. Any comments on this matter would be greatly appreciated, and I'll summarize the replies. Thanks in advance, Yangsoo Kim, Ph.D.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Aug 24 14:26:01 2007 From: "Indranil Rudra indranil.rudra+*+chemistry.gatech.edu" To: CCL Subject: CCL:G: C60 atomic coordinates with D3d symmetry Message-Id: <-35017-070824111403-4666-8gKjdetHRhF7uLUNniHBXA _ server.ccl.net> X-Original-From: "Indranil Rudra" Date: Fri, 24 Aug 2007 11:13:59 -0400 Sent to CCL by: "Indranil Rudra" [indranil.rudra{:}chemistry.gatech.edu] Dear colleagues, I was trying to obtain the atomic coordinates of C60 in D3d symmetry. I found from previous ccl mailing list the coordinates for D5d symmetry in gaussian z-matrix format but could not find for D3d symmetry. I was wondering if anyone could help me with the information ? Regards, Indranil Rudra Department of Chemistry and Biochemistry Georgia Institute of Technology Atlanta,GA From owner-chemistry@ccl.net Fri Aug 24 14:59:01 2007 From: "Andrew Orry andy-*-molsoft.com" To: CCL Subject: CCL: MolSoft ICM Workshop - Protein Structure and Drug Discovery - September 2007 Message-Id: <-35018-070824060311-15643-8q9ITy1fTy7pnOdSkMNtgg=server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 23 Aug 2007 09:49:03 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy-,-molsoft.com] Molsoft LLC (www.molsoft.com) would like to invite you to an ICM Workshop entitled "Protein Structure and Drug Discovery" to be held on September 20th � 21st 2007 in La Jolla, CA, USA. The workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate in this workshop. The workshop is presented by Prof. Ruben Abagyan (Scripps) and Dr. Maxim Totrov (MolSoft). This workshop consists of lectures, demonstrations and �hands-on� computational experiments and will cover: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, chemical clustering, searching, superposition ... - QSAR, machine learning - Protein-Protein Docking See www.molsoft.com/training.html for more information. �The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools.� Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy^molsoft.com or call (858)625 2000 ext.108. MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. From owner-chemistry@ccl.net Fri Aug 24 15:34:00 2007 From: "Shobe, David David.Shobe.]|[.sud-chemie.com" To: CCL Subject: CCL:G: CCL Thermochemical calculations from Gaussian output file Message-Id: <-35019-070824141451-24081-KJOdXVkl4zqCQ5ozch2dxg]|[server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 24 Aug 2007 20:14:37 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe^^sud-chemie.com] Yangsoo, You won't get an exact match to experimental values, if that's what's giving you concern. But you should be *close* to the experimental values if your calculations are good. Even when comparing theoretical to theoretical heats of formations calc'd at the same level of theory, you can get different answers depending on which reactions you use and which values for the "known" heats of formation (such as atomization energies or reference species like H2O(g) or CH4(g)) you use. The CBS* and G* methods (G2, G3, and their variants) are the easiest to use, since they do all the adding and most of the subtracting for you. Regards, --David Shobe -----Original Message----- > From: owner-chemistry===ccl.net [mailto:owner-chemistry===ccl.net] Sent: Friday, August 24, 2007 1:32 AM To: Shobe, David Subject: CCL:G: CCL Thermochemical calculations from Gaussian output file Sent to CCL by: "Yangsoo Kim" [vsmember%x%gmail.com] Dear all, Im wondering if anyone of you performed the thermochemical calculations > from Gaussian output. What wed like to do is to calculate heat of formation, ionization energy, electron affinity, proton affinity, and bond dissociation energy from Gaussian output files. We first tried to perform those calculations based on some published approaches (e.g., Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds, L. A. Curtiss, P. C. Redfern, and D. J. Frurip, Reviews of Computational Chemistry, Volume 15 Edited by K. B. Lipkowitz and D. B. Boyd pp.147-202). Unfortunately, our calculation results do not match the data that have been available in the computational thermochemistry literature. I'd appreciate if anyone can suggest how to get those thermochmical property values out of Gaussian output file. Due to our tight project schedule, it would be the best if any commercial or open (free) code or software is available. Any comments on this matter would be greatly appreciated, and I'll summarize the replies. Thanks in advance, Yangsoo Kim, Ph.D.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Aug 24 16:36:01 2007 From: "Michel Petitjean ptitjean[*]itodys.jussieu.fr" To: CCL Subject: CCL: Mol. modeling freewares / Sun computers Message-Id: <-35020-070824150114-22557-g/hHM0zXYbU0/cDjQSbwcA|*|server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 24 Aug 2007 21:01:03 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean#%#itodys.jussieu.fr] To: chemistry .. ccl.net Subj: Mol. modeling freewares / Sun computers Hi CCLers, I have generated versions of my freewares for Sun computers (binaries are available for both sparc and x64 architectures). Goto: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (needs a pairwise correspondence) ASV: Analytical calculation of van der Waals surfaces and volumes. CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (no need of a pairwise correspondence: it is computed) DOG: Docking Geometrically two molecules. (needs a pairwise correspondence) POP: Optimal Partition (classification) QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included) RADI: Computation of the Radius and Diameter of a spatial set (plus some other quantities) Please contact me for any question regarding these products. I thank the Sun company for providing adequate resources and I thank the ezqual/isv support team for technical assistance. Michel Petitjean, Email: petitjean .. itodys.jussieu.fr ITODYS (CNRS, UMR 7086) 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Fri Aug 24 17:11:01 2007 From: "Karol Langner karol.langner]^[kn.pl" To: CCL Subject: CCL:G: Thermochemical calculations from Gaussian output file Message-Id: <-35021-070824162157-28302-dptICmaajcF4SbQRZJHVMA++server.ccl.net> X-Original-From: Karol Langner Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 24 Aug 2007 21:16:22 -0400 MIME-Version: 1.0 Sent to CCL by: Karol Langner [karol.langner,+,kn.pl] On Friday 24 August 2007 11:24, Debellis Anthony CE US anthony.debellis^_^cibasc.com wrote: > Sent to CCL by: "Debellis Anthony CE US" [anthony.debellis|cibasc.com] > You might want to have a look at the white paper from Gaussian, Inc. > entitled "Thermochemistry in Gaussian". I'm sure it's available on > their website. > > Anthony DeBellis > Ciba Here is the link: http://www.gaussian.com/g_whitepap/thermo.htm -- written by Karol Langner Fri Aug 24 21:16:01 EDT 2007 From owner-chemistry@ccl.net Fri Aug 24 17:47:01 2007 From: "Thomas Heine thomas.heine[A]chemie.tu-dresden.de" To: CCL Subject: CCL:G: C60 atomic coordinates with D3d symmetry Message-Id: <-35022-070824163842-11092-fs3ipYqnN9UkmsREV0phLg[#]server.ccl.net> X-Original-From: "Thomas Heine" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 24 Aug 2007 21:35:59 +0200 MIME-Version: 1.0 Sent to CCL by: "Thomas Heine" [thomas.heine{}chemie.tu-dresden.de] Try Cage (http://www.math.uni-bielefeld.de/~CaGe/) to create coordinates but note that there is only one IPR for C60, and that is Ih. Regards, Thomas 2007/8/24, Indranil Rudra indranil.rudra+*+chemistry.gaech.edu : > > Sent to CCL by: "Indranil Rudra" [indranil.rudra{:}chemistry.gatech.edu] > Dear colleagues, > I was trying to obtain the atomic coordinates of C60 in D3d symmetry. I found from previous ccl mailing list the coordinates for D5d symmetry in gaussian z-matrix format but could not find for D3d symmetry. I was wondering if anyone could help me with the information ? > > Regards, > Indranil Rudra > Department of Chemistry and Biochemistry > Georgia Institute of Technology > Atlanta,GA> > > > From owner-chemistry@ccl.net Fri Aug 24 19:26:01 2007 From: "Jimmy Lawrence jlawrence%x%slb.com" To: CCL Subject: CCL:G: MFI, zeolite structure with Gaussian03 Message-Id: <-35023-070824192527-11743-MlJUHAopw/DOkg6TREUnHQ|a|server.ccl.net> X-Original-From: Jimmy Lawrence Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 24 Aug 2007 18:25:22 -0400 MIME-version: 1.0 Sent to CCL by: Jimmy Lawrence [jlawrence{:}slb.com] Hi CCL members, I am a beginner in calculating this type of system. Can somebody point a tutorial or share some experience by simple instruction on how to build the structure of MFI (or other zeolite) with PBC in Gaussian03 (via GaussView) and how to dock the molecule to evaluate (e.g. CO2) ? Thank you, Jimmy