From chemistry-request@server.ccl.net Wed Aug 28 04:25:48 2002 Received: from aspirine.u-strasbg.fr (IDENT:root@[130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7S8Plr21898 for ; Wed, 28 Aug 2002 04:25:47 -0400 Received: from pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g7S8FbL31095 for ; Wed, 28 Aug 2002 10:15:37 +0200 Message-ID: <3D6BCA43.2010602@pharma.u-strasbg.fr> Date: Tue, 27 Aug 2002 20:51:47 +0200 From: Antoine Logean User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; fr-FR; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: fr-fr MIME-Version: 1.0 To: "'chemistry@ccl.net'" Subject: Bioinformatic software development copanies in Zurich/Basel References: <3AA99E087354D61185E4002048403CFC59DFC9@irnts23.ifp.fr> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All, Who knows companies that develop softwares in bioinformatics and/or in molecular modeling around Zurich/Basel in Switzerland ? thank you Antoine From chemistry-request@server.ccl.net Wed Aug 28 08:47:32 2002 Received: from thor.chem.sdu.dk ([130.225.142.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SClVr30171 for ; Wed, 28 Aug 2002 08:47:31 -0400 Received: from localhost (tetz@localhost) by thor.chem.sdu.dk (SGI-8.9.3/8.9.3) with ESMTP id OAA08658 for ; Wed, 28 Aug 2002 14:49:36 +0200 (MDT) Date: Wed, 28 Aug 2002 14:49:36 +0200 From: Per Tetzschner Olsen To: chemistry@ccl.net Subject: Default DFT grid in gaussian 92 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL I am testing small transition states optimization jobs with reference data at the moment. Unfortunaly I am using Gaussian 98 and the reference (Houk et al.) used Gaussian 92. And I can not remember the default grid in Gaussian 92 for DFT (b3lyp/6-31g*) and I would appreciate if some of you have a better memory than I. DFT was not in the first gaussian 92 release as far as I can recall, but in a later release. In case you find the default grid for DFT in gaussian 94, please let me know. With regards Per Per Tetzschner Dept. of Chemistry University of Southern Denmark 5230 Odense M Denmark From chemistry-request@server.ccl.net Wed Aug 28 08:02:14 2002 Received: from pc15190.chemie.uni-marburg.de (root@[137.248.152.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SC2Er28474 for ; Wed, 28 Aug 2002 08:02:14 -0400 Received: from sg1503.chemie.uni-marburg.de (guest@sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by pc15190.chemie.uni-marburg.de (8.12.5/8.12.5/schn) with ESMTP id g7SC1qGe030281 for ; Wed, 28 Aug 2002 14:01:57 +0200 Received: from localhost (karin@localhost) by sg1503.chemie.uni-marburg.de (8.12.5/8.12.5/schn) with ESMTP id g7SC1xXg022748 for ; Wed, 28 Aug 2002 14:02:04 +0200 (MEST) Date: Wed, 28 Aug 2002 14:01:59 +0200 From: Karin Wichmann To: chemistry@ccl.net Subject: Summary: basis set extrapolation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g7SC2Er28475 Dear CCLers, this is a summary of answers I received to my question on basis set extrapolation. Many Thanks! Karin 1. from Jamie Platts Origin of Attraction and Directionality of the pi/pi Interaction: Model Chemistry Calculations of Benzene Dimer Interaction. Seiji Tsuzuki,* Kazumasa Honda, Tadafumi Uchimaru, Masuhiro Mikami, and Kazutoshi Tanabe, JACS 2002 (124) p104. The MP2 energy at the basis set limit was estimated by the method proposed by Feller.80 In Fellers method the calculated interaction energies were fitted to the form a + b exp(-cX) (where X is 2 for cc-pVDZ, 3 for cc-pVTZ, etc). The MP2 energy at the basis limit (EMP2(limit)) was then estimated by extrapolation. where ref. 80 is (80) Feller, D. J. Chem. Phys. 1992, 96, 6104. 2. from Stefan Fau there is an extrapolation scheme in Peterson, Woon, Dunning, J. Chem. Phys. 100, 7410 (1994), equation 2. For DZ, TZ, and QZ the "complete basis set" value is computed as: V(extr.) = [ cb2*(V3-b3'*V1) - cb3*(V2-b2'*V1) ] / [ cb2*(1-b3') - cb3*(1-b2') ] cbN = exp(-N^2) - exp(-N) bN' = exp(-(N-1)) N = X-1 (cc-pVXZ) V1 = V(cc-pVDZ) You should find that the extrapolated values from the cc-pVXZ and aug-cc-pVXZ series are very similar. They would be identical if the extrapolation were perfect since cc-pVXZ and aug-cc-pVXZ become identical in the limit of X -> inf. 3. from Juan Pablo Senosiain there ares several methods/models for performing the basis set extrapolations. Check out the references by T. Helgaker et al. e.g. J. chem. Phys. v112, pp.9229 4. from Johannes Weber several extrapolation procedures have been suggested in the literature. At the moment I have only one reference handy: D.Feller, K. A. Peterson, J.Chem.Phys. 108, 154 (1998). 5. from Christoph van Wüllen es gibt z.B. eine 2-Punkt-Extrapolationsformel von Truhlar, neben einigen anderen. (there is a 2-point extrapolation formula by Truhler, among others) References collected by myself are: J.Chem.Phys. 2001, 114, p.1974 (Feller and Sordo) J.Chem.Phys. 2000, 112, p.5604 (Sordo) My question was: > I have done CCSD(T) single point calculations with cc-pVXZ (X=D,T,Q) and > aug-cc-pVXZ (X=D,T) basis sets for several structures on a reaction > path. Now I would like to know whether it is possible to do a basis set > extrapolation from these data and if so, how is it to be done > explicitly? From chemistry-request@server.ccl.net Wed Aug 28 10:42:58 2002 Received: from purple.csi.cam.ac.uk ([131.111.8.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SEgwr01989 for ; Wed, 28 Aug 2002 10:42:58 -0400 Received: from ursus.ch.cam.ac.uk ([131.111.121.19] helo=ursus.cam.ac.uk) by purple.csi.cam.ac.uk with esmtp (Exim 4.10) id 17k425-0001V6-00; Wed, 28 Aug 2002 15:42:57 +0100 Message-Id: <5.1.1.6.0.20020828153459.031e8750@hermes.cam.ac.uk> X-Sender: pm286@hermes.cam.ac.uk (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Wed, 28 Aug 2002 15:42:16 +0100 To: "Martin, Eric" , chemistry@ccl.net From: Peter Murray-Rust Subject: Re: CCL:XML and combinatorial chemistry In-Reply-To: <76914E341621D611ADB5000102758978675E8B@emvshiva.chiron.com > Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed At 16:50 27/08/2002 -0700, Martin, Eric wrote: >Dear CCL, > >Does CML or any other chemical XML application support combinatorial >chemistry? Specifically, I have in mind Markush or generic structures with >lists of R groups. Is specific support for Markush structures necessary or >useful, or is there a way to do it with existing CML elements? The CML FAQ >(http://www.xml-cml.org/faq/index.html) notes that "Heteromers" e.g. >modified proteins, are difficult to represent, which suggests a Markush may >be as well. Thanks in advance. A superset of CML (CMLQuery) is being developed to support generic structures. (Queries and Markush are very similar as they represent a set of compounds rather than a single one.) The criteria we try to adopt for any new addition to CML include: - does it cover a wide range of current practice? - is it possible to support it in software? It must be relatively easy to implement and we need a working example before we feel happy about adding a feature. Best P. (If you have a particular application in mind I would be happy to be mailed off-list). >Regards, Eric >___________________ > >Eric Martin >Chiron Corp, LSC 4.250 >4560 Horton St. >Emeryville, CA 94608 >(510)923-3306 >FAX 923-2010 > From chemistry-request@server.ccl.net Wed Aug 28 00:12:39 2002 Received: from mercury.chem.northwestern.edu (root@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7S4Cdr14033 for ; Wed, 28 Aug 2002 00:12:39 -0400 Received: from HaitaoJI (che116250.chem.northwestern.edu [129.105.116.250]) by mercury.chem.northwestern.edu (8.11.6+Sun/8.11.3) with SMTP id g7S4Cal29033 for ; Tue, 27 Aug 2002 23:12:36 -0500 (CDT) Message-ID: <001f01c24e49$24cf4de0$9865fea9@HaitaoJI> From: "Haitao Ji" To: Subject: sphgen Date: Tue, 27 Aug 2002 22:12:37 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01C24E16.DA00FCA0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C24E16.DA00FCA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, DOCK user Does anyone learn how to add the strutural information of ligands from = the crystal structure into the resulting file of sphgen (that is *.sph)? = I think the ligand coordinates are easy to be added into the *.sph file. = But how can we determine the sphere redius for those atoms from the = crystal structure? Besides, How can we designate the number of the atom = with which suface atoms are associated?=20 Could anyone share me with his experience in sphere generation? Any = suggestion is appreciated. Haitao Ji jihaitao@chem.nwu.edu ------=_NextPart_000_001C_01C24E16.DA00FCA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, DOCK user
 
Does anyone learn how to add the = strutural=20 information of ligands from the crystal structure into the resulting = file of=20 sphgen (that is *.sph)? I think the ligand coordinates are easy to = be added=20 into the *.sph file. But how can we determine the sphere redius for = those atoms=20 > from the crystal structure? Besides, How can we designate the = number=20 of the atom with which suface atoms are associated?
 
Could anyone share me with his = experience in sphere=20 generation? Any suggestion is appreciated.
 
Haitao Ji
jihaitao@chem.nwu.edu
 
------=_NextPart_000_001C_01C24E16.DA00FCA0-- From chemistry-request@server.ccl.net Wed Aug 28 11:13:15 2002 Received: from fletxa.iqs.es (root@[193.145.86.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SFDEr03022 for ; Wed, 28 Aug 2002 11:13:15 -0400 Received: from pcb129 (iqstac86.iqs.url.es [193.145.86.169]) by fletxa.iqs.es (8.9.3/8.9.3) with SMTP id RAA03972 for ; Wed, 28 Aug 2002 17:32:40 +0200 Message-ID: <01dd01c24eb5$ae3a5220$a95691c1@jhinst.cas.cz> From: =?iso-8859-1?Q?Oscar_Rey_i_Puiggr=F2s?= To: Subject: SCRF Date: Wed, 28 Aug 2002 19:09:33 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01DA_01C24EC6.71892660" 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 This is a multi-part message in MIME format. ------=_NextPart_000_01DA_01C24EC6.71892660 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: I'm trying to calculate solvation energy of a set of systems using G98. = I've seen that PCM model shows many contributions to this solvation = energy and solvation energy value itself, while IPCM and SCI-PCM only = gives a final energy but neither any solvation energy nor any = contribution to that energy is printed in the output file. Could anybody = tell me how can I extract solvation energy from an IPCM or SCI-PCM = calculation output? Many thanks Oscar ______________________________________________________ Oscar Rey i Puiggr=F2s Grup de Qu=EDmica Computacional (Grup d'Enginyeria Molecular_GEM) Institut Qu=EDmic de Sarri=E0, Universitat Ramon Llull Telf. 93 267 20 00 Ext. 356 e-mail orey@iqs.edu Via Augusta 390, 08017 Barcelona_CATALUNYA ------=_NextPart_000_01DA_01C24EC6.71892660 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear netters:
 
I'm trying to calculate solvation energy of a = set of=20 systems using G98. I've seen that PCM model shows many contributions to = this=20 solvation energy and solvation energy value itself, while IPCM=20 and SCI-PCM only gives a final energy but neither any solvation = energy nor=20 any contribution to that energy is printed in the output file. Could = anybody=20 tell me how can I extract solvation energy from an IPCM = or SCI-PCM=20 calculation output?
 
Many thanks
 
Oscar

______________________________________________________Oscar=20 Rey i Puiggr=F2s
Grup de Qu=EDmica Computacional (Grup d'Enginyeria=20 Molecular_GEM)
Institut Qu=EDmic de Sarri=E0, Universitat Ramon = Llull
Telf. 93=20 267 20 00 Ext. 356
e-mail orey@iqs.edu
Via Augusta 390, 08017=20 Barcelona_CATALUNYA
------=_NextPart_000_01DA_01C24EC6.71892660-- From chemistry-request@server.ccl.net Wed Aug 28 10:17:39 2002 Received: from internal.cambridgesoft.com ([198.112.109.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SEHdr01186 for ; Wed, 28 Aug 2002 10:17:39 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: XML and combinatorial chemistry X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 Date: Wed, 28 Aug 2002 10:17:34 -0400 Message-ID: <4F7EC9B21FB40043A33952CF23582FE986EB@EXCHANGE.camsoft.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: XML and combinatorial chemistry Thread-Index: AcJOmKobtxcOQ61VTDmSzk/UPEmJKgAA4jJQ From: "Stew Rubenstein" To: , , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g7SEHer01187 ChemDraw, ChemOffice, and other CambridgeSoft tools support XML representations and combinatorial chemistry. This also includes our library enumerator, plate inventory, BioAssay HTS, E-Notebook, and other applications. Please contact info@cambridgesoft.com to talk about this in more detail. -Stew Rubenstein President and CTO CambridgeSoft Corp. > -----Original Message----- > From: Shobe, Dave [mailto:dshobe@SUD-CHEMIEINC.COM] > Sent: Wednesday, August 28, 2002 9:36 AM > To: CHMINF-L@LISTSERV.INDIANA.EDU > Subject: FW: XML and combinatorial chemistry > > > Maybe someone in this community can answer this. Please reply to Eric > Martin directly as he might not read CHMINF-L regularly. > > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Don't bother flaming me: I'm behind a firewall. > > > > -----Original Message----- > From: Martin, Eric [mailto:Eric_Martin@chiron.com] > Sent: Tuesday, August 27, 2002 7:51 PM > To: chemistry@ccl.net > Subject: CCL:XML and combinatorial chemistry > > > Dear CCL, > > Does CML or any other chemical XML application support combinatorial > chemistry? Specifically, I have in mind Markush or generic > structures with > lists of R groups. Is specific support for Markush structures > necessary or > useful, or is there a way to do it with existing CML > elements? The CML FAQ > (http://www.xml-cml.org/faq/index.html) notes that "Heteromers" e.g. > modified proteins, are difficult to represent, which suggests > a Markush may > be as well. Thanks in advance. > > Regards, Eric > ___________________ > > Eric Martin > Chiron Corp, LSC 4.250 > 4560 Horton St. > Emeryville, CA 94608 > (510)923-3306 > FAX 923-2010 > > > > CHMINF-L Archives (also to join or leave CHMINF-L, etc.) > http://listserv.indiana.edu/archives/chminf-l.html > Search the CHMINF-L archives at: > http://listserv.indiana.edu/cgi-bin/wa?S1=chminf-l > Sponsors of CHMINF-L: > http://www.indiana.edu/~cheminfo/chminf-l_support.html > From chemistry-request@server.ccl.net Wed Aug 28 12:56:03 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SGu3r07033 for ; Wed, 28 Aug 2002 12:56:03 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id g7SGu2m21050 for ; Wed, 28 Aug 2002 12:56:02 -0400 (EDT) Date: Wed, 28 Aug 2002 12:56:02 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net Subject: 02.10.07 SURA Comput Chem Workshop, U Kentucky, Lexington Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT Date: Wed, 28 Aug 2002 11:52:58 -0400 From: John Connolly Subject: Can you post this announcement? Thanks SURA Computational Chemistry Workshop Software Solutions to Large Scale Problems in Computational Chemistry University of Kentucky, Lexington, Kentucky October 7 & 8, 2002 The theme of the conference will be to examine alternatives for mapping computational chemistry software on to the new generation of Terascale machines. For example, the National Science Foundation is building the ETF (Extended Terascale Facility) sometimes known as the Teragrid, which will consist of thousands of processors connected by a 40 Gigabit network with links of several thousands of miles between sites. The key question for computational chemistry is “Will future computational chemistry be able to take advantage of the Teragrid to solve very large scale problems?” This conference will examine current and future computational chemistry techniques and software, such as quantum chemistry, molecular dynamics, materials research, biology and bioinformatics. Several of the leading researchers in these fields have committed to attend and make presentations, either in Lexington or over the Internet through the use of the Access Grid Network.. See the following web site for details and registration. http://www.sura.org/events/2001/compchem/chemistry02.html From chemistry-request@server.ccl.net Wed Aug 28 13:50:03 2002 Received: from bute.st-andrews.ac.uk (root@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SHo2r08839 for ; Wed, 28 Aug 2002 13:50:02 -0400 Received: from superintendentchalmers.st-andrews.ac.uk (bmspc-glt2-9 [138.251.94.76]) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id SAA27546 for ; Wed, 28 Aug 2002 18:44:21 +0100 (BST) Message-Id: <5.1.1.6.0.20020828182638.00a4f548@bute.st-andrews.ac.uk> X-Sender: im17@bute.st-andrews.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Wed, 28 Aug 2002 18:51:14 +0100 To: chemistry@ccl.net From: "Ibrahim M.Moustafa" Subject: Docking and binding affinity Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL users, I have other questions concerning docking experiment. Is there any correlation between the binding constant, Ki, of the ligand and the ability of the docking program to predict its interaction with the binding site? Is there a lower limit for the binding constant below which predicting the ligand position becomes more difficult?? Can we predict the binding of carbohydrate ligands which usually have binding affinity in the mM range? I wonder if people consider the binding constant when they select a set of ligands to validate their docking programs or they don't. Do they include ligands with low affinities in the testing set? Appreciated any comment to clarify this point. Thanks for your help. Ibrahim Ibrahim M.Mostafa Center for Biomolecular Sciences, Molecular Sciences Building, North Haugh,St.Andrews, Fife,KY16 9ST, Scotland,U.K. Tel. +44-1334-467257 Fax +44-1334-462595 e-mail: im17@st-Andrews.ac.uk From chemistry-request@server.ccl.net Wed Aug 28 17:30:29 2002 Received: from sherman.che.utexas.edu ([128.83.162.80]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SLUTr15786 for ; Wed, 28 Aug 2002 17:30:29 -0400 Received: from einstein.che.utexas.edu (einstein.che.utexas.edu [128.83.162.4]) by sherman.che.utexas.edu (8.10.1/8.10.1) with ESMTP id g7SLUTu29274 for ; Wed, 28 Aug 2002 16:30:29 -0500 (CDT) Received: from localhost (wang@localhost) by einstein.che.utexas.edu (8.11.6/8.11.6) with ESMTP id g7SLQCF23508 for ; Thu, 29 Aug 2002 03:26:12 +0600 X-Authentication-Warning: einstein.che.utexas.edu: wang owned process doing -bs Date: Thu, 29 Aug 2002 03:26:12 +0600 (GMT-6) From: Yun Wang To: chemistry@ccl.net Subject: Band structure of surface In-Reply-To: <5.1.1.6.0.20020828182638.00a4f548@bute.st-andrews.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Dear CCLers, I plan to calculate the band structure of the surface. Could someone tell me how to choose the high-symmetry k-points, and where to find the coordinate for these k-points. Is there any website about this topic? I have searched them by google, but there are little useful informations. Thanks for you reply. I shall summary it later. Best regards! sincerely. Yun Wang