From chemistry-request@server.ccl.net Mon Apr 9 02:02:42 2001 Received: from cpc.pp.molsci.csiro.au (firewall-user@[138.194.241.18]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f3962fD07169 for ; Mon, 9 Apr 2001 02:02:41 -0400 Received: by cpc.pp.molsci.csiro.au; id PAA01737; Mon, 9 Apr 2001 15:50:35 +1000 Received: from tigger.pp.molsci.csiro.au(138.194.245.49) by cpc.pp.molsci.csiro.au via smap (V4.2) id xma001701; Mon, 9 Apr 01 15:50:27 +1000 Received: from localhost (bra369@localhost) by tigger.pp.molsci.csiro.au (8.9.3+Sun/8.9.3) with SMTP id PAA05220 for ; Mon, 9 Apr 2001 15:28:22 +1000 (EST) Date: Mon, 9 Apr 2001 15:28:22 +1000 (EST) From: Kim Branson To: chemistry@ccl.net Subject: distributed pharmacophore searching Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers I'm looking for a program that is able to query a database(s) of small molecules for compounds that have characteristics of a pharmacophore. I know things like unity exist and that sort of functionality would be useful, however i plan to run such code on a linuc based beowulf cluster. Has anyone heard of/used any tools for a such a purpose and found them useful? regards Kim Branson ______________________________________________________________________ Mr Kim Branson Phd Student Structural Biology Walter and Eliza Hall Institute Royal Parade, Parkville, Melbourne, Victoria Ph 61 03 9662 7136 Email kim.branson@bioresi.com.au ______________________________________________________________________ From chemistry-request@server.ccl.net Mon Apr 9 05:03:15 2001 Received: from yangtze.hku.hk (IDENT:root@[147.8.148.244]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3993AD08727 for ; Mon, 9 Apr 2001 05:03:11 -0400 Received: from localhost (andy@localhost) by yangtze.hku.hk (8.9.3/8.9.3) with ESMTP id RAA14641 for ; Mon, 9 Apr 2001 17:11:26 +0800 Date: Mon, 9 Apr 2001 17:11:26 +0800 (HKT) From: Ng Man Fai To: Subject: Ethylene absorption peak. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone, May I ask the first optical absorption peak of ethylene in gas phase is 8.1eV or 7.2eV? I got 7.2eV from ZINDO/G98, however, I got 8.1eV in some other papers. I am not sure do they refer to the same peak. Thanks for your kindly help. Regards, Andy From chemistry-request@server.ccl.net Mon Apr 9 07:16:20 2001 Received: from bioinfo.ernet.in ([202.41.70.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f39BGJD11135 for ; Mon, 9 Apr 2001 07:16:19 -0400 Received: from localhost (manjari@localhost) by bioinfo.ernet.in (8.8.7/8.8.7) with ESMTP id QAA06936 for ; Mon, 9 Apr 2001 16:40:09 +0530 Date: Mon, 9 Apr 2001 16:40:09 +0530 (IST) From: To: chemistry@ccl.net Subject: Van der Waals contacts Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am interestedin calculating the van der waals contacts in some pdb entries. can u please suggest me any free programs that are available for this purpose. Also if there is a way to determine the van der waals contacts using InsightII(ver 95) i would be greatful. regards Sunitha Manjari Bioinformatics centre Pune Univ India From chemistry-request@server.ccl.net Sun Apr 8 11:45:56 2001 Received: from relay3.inwind.it ([212.141.53.74]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f38FjuD02100 for ; Sun, 8 Apr 2001 11:45:56 -0400 Received: from mircomputer (62.98.225.117) by relay3.inwind.it (5.5.025) id 3ACAF420000AD8FA for chemistry@ccl.net; Sun, 8 Apr 2001 17:42:47 +0200 Message-ID: <00a201c0c042$3e28a700$cbd6623e@mircomputer> From: "Mirco Meniconi" To: Subject: semiempirical Date: Sun, 8 Apr 2001 17:40:29 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_009F_01C0C053.0101FD20" 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_009F_01C0C053.0101FD20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hy all, I need to calculate the interaction between a molecule target and a = probes like H2O, O, etc. (the same thing I can do with GRID program) by = using semiempiricals ethods (and ab-initio). It is possible do this wtih Gaussian, Mopac or Ampac? if Yes, how can I do? tanks in advance mirco ------=_NextPart_000_009F_01C0C053.0101FD20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hy all,
I need to calculate the interaction = between a=20 molecule target and a probes like H2O, O, etc. (the same thing I = can do=20 with GRID program) by using semiempiricals ethods (and=20 ab-initio).
It is possible do this wtih Gaussian, = Mopac or=20 Ampac?
if Yes, how can I do?
tanks in advance
 
mirco
------=_NextPart_000_009F_01C0C053.0101FD20-- From chemistry-request@server.ccl.net Mon Apr 9 05:43:38 2001 Received: from mlucom8.urz.uni-halle.de ([141.48.10.118]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f399hcD08994 for ; Mon, 9 Apr 2001 05:43:38 -0400 Received: from studcom.urz.uni-halle.de by mlucom8.urz.uni-halle.de with lsmtp with ESMTP; Mon, 9 Apr 2001 11:41:27 +0200 Received: from hmo (hmo.chemie.Uni-Halle.DE [141.48.79.172]) by studcom.urz.uni-halle.de (8.9.3 (PHNE_22672)/8.9.3) with SMTP id LAA13239 for ; Mon, 9 Apr 2001 11:41:26 +0200 (METDST) From: Bernd Schubert To: chemistry@ccl.net Subject: gaussian and hollerith string Date: Mon, 9 Apr 2001 11:40:12 +0000 X-Mailer: KMail [version 1.1.99] Content-Type: Multipart/Mixed; boundary="------------Boundary-00=_0FWIOF1KN30URL07QYCN" MIME-Version: 1.0 Message-Id: <01040911401200.00984@hmo> --------------Boundary-00=_0FWIOF1KN30URL07QYCN Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 8bit Dear CCLers, I need some help with gaussian and the hollerith string for iop(2/19). I want to tell Gaussian98A7 to use a lower point group than my molecule has, in detail my molecule has C2V symmetry but I only want to use CS symmetry. So I think I have to say iop(2/19=2HCS) in the input line. But I get the message about a syntax error. I also tried to use quots but no success. Furthermore I don't understand what iop(2/20) means. It is in relation to iop(2/19) but I really don't understand what they want to tell me about it. Thanks in advance, Bernd PS: my input file is attached to the mail --------------Boundary-00=_0FWIOF1KN30URL07QYCN Content-type: text/english; name="060.inp" Content-transfer-encoding: 8bit Content-Disposition: attachment; filename="060.inp" %mem=52428800 %chk=oci.chk %nproc=1 #P ub3lyp/cc-pvtz popt(AddRedundant,Calcall,MaxCyc=50) SCF(MaxCyc=300) iop(2/16=3,2/19=2HCS) symm=loose Calculation of the oxiren, uhf, cs-symmetry 0 1 c c 1 cc2 h 2 hc3 1 hcc3 h 1 hc4 2 hcc4 3 dih4 o 1 oc5 2 occ5 3 dih5 cc2 1.450000 hc3 1.089000 hcc3 140.000 hc4 1.089000 hcc4 140.000 dih4 0.000 oc5 1.400000 occ5 60.000 dih5 180.000 5 2 1 60.0 F 5 1 2 60.0 F --------------Boundary-00=_0FWIOF1KN30URL07QYCN-- From chemistry-request@server.ccl.net Mon Apr 9 08:27:46 2001 Received: from matavnet.hu ([195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f39CRjD13458 for ; Mon, 9 Apr 2001 08:27:45 -0400 Received: (qmail 9683 invoked from network); 9 Apr 2001 14:27:42 +0200 X-Spam-Warning: line-219-10.dial.matav.net is in the DUL Received: from line-219-10.dial.matav.net (HELO chemaxon.com) (145.236.219.10) by mail.matavnet.hu with SMTP; 9 Apr 2001 14:27:43 +0200 Message-ID: <3AD1AAF3.3DA2DE0F@chemaxon.com> Date: Mon, 09 Apr 2001 14:28:35 +0200 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.51 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, chemweb@ic.ac.uk Subject: New releases: Marvin 2.7.6 and JChem/JKlustor 1.5.4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please excuse multiple postings. Hi, Marvin Applets and Marvin JavaBeans 2.7.6, JChem and JKlustor 1.5.4 have been released. The packages contain applications and development tools. - Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects. - JChem provides chemical database searching capabilities by integration into relational database engines supporting SQL. - JKlustor is a clustering software that can generate and apply 2D molecular fingerprints. Marvin Applets are free for free web sites. MarvinSketch and MarvinView applications are free for academic and home users. NEW FEATURES: New features in recent releases of Marvin: - Faster and improved 2D coordinate calculation (cleaning) from SMILES/2D/3D input - Animations (http://www.chemaxon.com/marvin/doc/example-view3.2.html - please be patient. It takes some time to download the applet and input of the animations.) - XYZ and Extended (V3) Molfile import - Text field component for tables - Preloading and caching molecules - MarvinView application also displays text fields (from SDfiles) - MarvinSketch application saves to / loads from multi-molecule files - Workarounds for Netscape 6 - Fixes - Etc... (http://www.chemaxon.com/marvin/news.html) New features in recent releases of JChem: - New clustering module: JKlustor http://www.jchem.com/doc/admin/JKlustor.html - Improved compatibility with the Interbase Server product of Inprise. - JChemManager (jcman) and JChemSearch (jcsearch) are also available as command line utilities. - Includes the latest Marvin version - Fixes - Etc... (see http://www.jchem.com/changes.html) The software can be tried/downloaded at http://www.chemaxon.com/products.html Regards, Ferenc -- Dr. Ferenc Csizmadia Managing Director ChemAxon Ltd. http://www.chemaxon.com mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Mon Apr 9 14:43:47 2001 Received: from phobos.email.Arizona.EDU (IDENT:root@[128.196.133.165]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f39IhlD17741 for ; Mon, 9 Apr 2001 14:43:47 -0400 Received: from demetrio.ifi.unicamp.br (128.196.86.129) by phobos.email.Arizona.EDU (5.1.056) id 3ACA79EF0006C442 for chemistry@ccl.net; Mon, 9 Apr 2001 11:43:46 -0700 Message-Id: <5.0.2.1.0.20010409233831.02111390@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Mon, 09 Apr 2001 23:42:17 -0700 To: chemistry@ccl.net From: Demetrio Antonio da Silva Filho Subject: .RES files Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, I have some .res files with the unit cell of some crystals and I am looking for a software to open those files and build the crystals. Does anybody knows if there is any free software (or not) to do that? Any hints will be welcome! Demetrio Filho From chemistry-request@server.ccl.net Mon Apr 9 16:20:41 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f39KKfD18937 for ; Mon, 9 Apr 2001 16:20:41 -0400 Received: from demetrio.ifi.unicamp.br (128.196.86.129) by deimos.email.Arizona.EDU (5.1.056) id 3AB8AE98001881BB for CHEMISTRY@ccl.net; Mon, 9 Apr 2001 13:20:40 -0700 Message-Id: <5.0.2.1.0.20010410011228.00b1c040@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Tue, 10 Apr 2001 01:19:12 -0700 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: .Res files and Molden Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, >Ali Rachid and Frederick Arnold advise me to use Molden to open the .Res files. Using molden I can open the .res files and I can create a small crystal, asking the program to create multiple cells. But the number of the cells that molden creates is not enough for my purposes. So, does anybody knows if it is possible to increase the number of cells plotted using molden? Or if there is a way to multiply those cells merging files? Thanks in advance, Demetrio Filho