From chemistry-request@ccl.net Thu Sep 25 03:24:19 2003 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8P7NlmK020289 for ; Thu, 25 Sep 2003 03:23:47 -0400 To: chemistry|at|ccl.net Subject: conformation analysis in Cerius2 MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy|at|givaudan.com Date: Thu, 25 Sep 2003 09:20:26 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.07a |May 14, 2001) at 25/09/2003 09:23:50, Serialize complete at 25/09/2003 09:23:50 Content-Type: multipart/alternative; boundary="=_alternative 00285311C1256DAC_=" X-Spam-Status: No, hits=2.3 required=7.0 tests=HTML_10_20,HTML_MESSAGE,NO_REAL_NAME version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 00285311C1256DAC_= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, I want to measure distances between two atoms of each conformers of a=20 molecule. Conformers have been generated by Cerius2. Radii of gyrasion,=20 energies, tags are loaded into the conformation table but structures not.=20 Thus one can not insert and calculate distances (like in MOE and Sybyl) in = this table.. What can I do? How can I extract the generated conformer=20 structures into a table or and an SD file? Many thank, Andr=E1s Borosy --=_alternative 00285311C1256DAC_= Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,


I want to measure distances between =  two atoms of each conformers of a molecule. Conformers have been gene= rated by Cerius2. Radii of gyrasion, energies, tags are loaded into the con= formation table but structures not. Thus one can not insert and calculate d= istances (like in MOE and Sybyl) in this table.. What can I do? How can I e= xtract the generated conformer structures into a table or and an SD file?

Many thank,

Andr=E1s Borosy
--=_alternative 00285311C1256DAC_=-- From chemistry-request@ccl.net Wed Sep 24 23:23:09 2003 -0400 Return-Path: dxl{at}mail.ustc.edu.cn Message-Id: <200309250319.LAA28055{at}mx1.ustc.edu.cn> Date: Thu, 25 Sep 2003 11:21:11 +0800 From: dxl{at}mail.ustc.edu.cn To: chemistry{at}ccl.net Subject: Fw: TDDFT how to determine the spin multiplicity Dear CCL#: I have a problem when I do a TDDFT calculation. Then ground state is a singlet, but the calculation must be do with UB3LYP, for it has a RHF#->UHF instability. ( #UB3LYP/gen TD(nstates=10) ) The result is Excited State 1: ?Spin -A" 0.3210 eV 3862.42 nm f=0.0000 I want to know how to determine the multiplicity whether it is singlet or triplet. Thank you for your help! Ding Xunlei 2003-09-25 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl{at}mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl = = = = = = = = = = = = = = = = = = = = From chemistry-request@ccl.net Thu Sep 25 09:30:45 2003 Received: from mailgate.tripos.com (mailgate.tripos.com [192.160.145.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8PDUEmK005489 for ; Thu, 25 Sep 2003 09:30:14 -0400 Message-ID: <3F72EDE4.2E524F11{at}tripos.com> From: David Larson To: chemistry{at}ccl.net Reply-To: bclark{at}tripos.com Date: Thu, 25 Sep 2003 08:30:12 -0500 Subject: Call for Papers MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="--=_NextPart_ST_08_30_13_Thursday_September_25_2003_4781" X-Accept-Language: en Sender: dlarson{at}tripos.com Organization: Tripos, Inc. http://www.tripos.com X-Spam-Status: No, hits=0.3 required=7.0 tests=MIME_BOUND_NEXTPART,X_ACCEPT_LANG version=2.55 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_ST_08_30_13_Thursday_September_25_2003_4781 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ************************************************************************** GETTING IT RIGHT: VARIABLE SELECTION AND MODEL VALIDATION IN (Q)SAR Spring National ACS Meeting in Anaheim CA (28 March - 1 April 2004) Sponsored by the Division of Computers in Chemistry (COMP) and by the QSAR and Modelling Society ************************************************************************** Despite the ascendance of combinatorial chemistry, high throughput screening, and various 'omics technologies in recent years, delineating structure/property relationships remains key to effective drug discovery. The models in question may be quantitative ones relating structure to biochemical activity (QSARs) or to some physical property (QSPRs), or they may be more qualitative, as in many in silico ADME/Tox applications. Whether the tool used is linear regression or PLS, discriminant analysis or SIMCA, a support vector machine or a neural net, there is always an over-arching need to pick appropriate variables as input to the model and to get some sense of how much confidence one can have in the model(s) produced. The general topic of variable selection and validation in (Q)SAR will form the basis of a multi-session symposium at the Spring 2004 meeting of the American Chemical Society in Anaheim CA. Methods development papers are welcome, as are abstracts for any application that involves variable selection or validation in some way. Selected papers will be considered for inclusion in a special "Perspectives in Drug Discovery and Design" ("PD3") issue of the Journal of Computer-Aided Molecular Design. If you would like to present a paper on some aspect of QSAR, QSPR, or a related area of chemometrics, please use the OASYS system to do so: http://oasys.acs.org/acs/227nm/comp/papers/index.cgi to submit your abstract directly. The deadline for submission is 17 November 2003. Bob Clark (bclark{at}tripos.com) Tripos, Inc. 1699 S. Hanley Road St. Louis MO 63144 ----=_NextPart_ST_08_30_13_Thursday_September_25_2003_4781 Content-Type: text/x-vcard; charset=us-ascii; name="dlarson.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="dlarson.vcf" Content-Description: Card for David Larson begin:vcard n:Larson;David A. tel;fax:314-647-9241 tel;work:314-951-3318 x-mozilla-html:FALSE org:TRIPOS, Inc. adr:;;1699 S. Hanley Road;St. Louis;MO;63144; version:2.1 email;internet:dlarson{at}tripos.com title:Senior Support Scientist note;quoted-printable:Please Send Requests For Technical=0D=0ASupport to 'support{at}tripos.com'.=0D=0ASYBYL 6.9/UNITY 4.4 for LINUX is now shipping! x-mozilla-cpt:;-26912 fn:David Larson end:vcard ----=_NextPart_ST_08_30_13_Thursday_September_25_2003_4781-- From chemistry-request@ccl.net Thu Sep 25 10:50:00 2003 Received: from uni-freiburg.de (ms.ruf.uni-freiburg.de [132.230.2.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8PEnqmK010287 for ; Thu, 25 Sep 2003 10:49:55 -0400 Received: from [132.230.171.124] (account ) by uni-freiburg.de (CommuniGate Pro WebUser 4.0.6) with HTTP id 12961133 for ; Thu, 25 Sep 2003 16:49:50 +0200 From: "Thomas Steinbrecher" Subject: CCL: Database for virtual screening To: chemistry{at}ccl.net X-Mailer: CommuniGate Pro Web Mailer v.4.0.6 Date: Thu, 25 Sep 2003 16:49:50 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, I am looking for a database of (preferably purchasable) chemical compounds that allows me to search for molecules by certain criteria (mol. weigth, number of N-atoms...) and save the resulting sets in a format suitable for computational chemistry programs (pdb, mol2..) to perform a search for potentially active compounds by docking. Is there a free database I can use? If not, what are commonly used databases for such a task and which are recommended? Thank you in advance for any comments, Thomas Steinbrecher Institut f|r physikalische Chemie Albertstr. 23a 79108 Freiburg From chemistry-request@ccl.net Thu Sep 25 10:40:30 2003 Received: from bmbpcu21.leeds.ac.uk (bmbpcu21.leeds.ac.uk [129.11.110.201]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8PEdwmK009747 for ; Thu, 25 Sep 2003 10:39:59 -0400 Received: from peter by bmbpcu21.leeds.ac.uk with local (Exim 3.22 #1) id 1A2YCS-0000Sz-00 for chemistry:at:ccl.net; Thu, 25 Sep 2003 15:38:36 +0000 Content-Type: text/plain; charset="iso-8859-15" From: Peter Oledzki Reply-To: peter:at:bioinformatics.leeds.ac.uk To: chemistry:at:ccl.net Subject: Parameters for GRID force-field calculations Date: Thu, 25 Sep 2003 15:38:36 +0000 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <03092515383600.01760@bmbpcu21> Content-Transfer-Encoding: 8bit Sender: Peter Oledzki X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLer's Does anybody possess the GRID force field probe parameters for the calcium ions and manganese ions? I seem to be missing these from my list of parameters for my docking calculations. Also has anybody had experiences with other force-fields (AMBER??) that would contain relevant parameters for my calculations. Thanks in advance for any help anybody can give me. I'll summarise the replies. Cheers Peter -- *********************************************************** Peter Oledzki PhD Bioinformatics Research Student School of Biochemistry and Molecular Biology University of Leeds LS2 9JT 0113 3432988 From chemistry-request@ccl.net Thu Sep 25 14:48:46 2003 Received: from sas.asc.hpc.mil (sas.asc.hpc.mil [140.31.140.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8PImEmK020243 for ; Thu, 25 Sep 2003 14:48:14 -0400 Received: from asc.hpc.mil (wk64.asc.hpc.mil [140.31.142.64]) by sas.asc.hpc.mil (8.12.10/8.12.10) with ESMTP id h8PImBQD119465 for ; Thu, 25 Sep 2003 14:48:12 -0400 (EDT) Message-ID: <3F73386B.8080600..at..asc.hpc.mil> Date: Thu, 25 Sep 2003 14:48:11 -0400 From: XIAOFENG FRANK DUAN Organization: CSC User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030716 X-Accept-Language: en-us, zh-cn MIME-Version: 1.0 To: CHEMISTRY..at..ccl.net Subject: GUI for VASP Content-Type: text/plain; charset=us-ascii; 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) Dear CCLers: Does anyone know any GUIs (free or commercial) for VASP which run on UNIX? Any info will be appreciated! Frank -- Xiaofeng Frank Duan, Ph.D | Phone: 937-904-8307 Sr. Application Analyst | Fax: 937-255-2288 ASC MSRC | Email: duanx..at..asc.hpc.mil Wright-Patterson AFB | URL: www.asc.hpc.mil