From laurent@crypt.u-strasbg.fr Mon May 26 02:44:48 1997 Received: from crypt.u-strasbg.fr for laurent@crypt.u-strasbg.fr by www.ccl.net (8.8.3/950822.1) id CAA02050; Mon, 26 May 1997 02:35:55 -0400 (EDT) Received: (from laurent@localhost) by crypt.u-strasbg.fr (951211.SGI.8.6.12.PATCH1042/8.6.10) id RAA14016; Sun, 25 May 1997 17:26:02 +0200 Date: Sun, 25 May 1997 17:26:02 +0200 (MET) From: Laurent TROXLER cc: chemistry@www.ccl.net Subject: Re: CCL:G:GAUSSIAN HOTLINE? In-Reply-To: <199705231543.LAA21002@alchemy.chem.utoronto.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > 1997 May 23 > CCL AS GAUSSIAN HOTLINE > > I think it's a matter of balance. Gaussian users should read the manual first > (manual--a kind of book), _then_ if necessary contact Gaussian; if that > does not work, then I think it's reasonable to resort to the CCL. We should > remember that Gaussian is the most widely-used program for doing computational > chemistry (the most widely-used ab initio program anyway), so it seems almost > natural that on a _computational _chemistry_ list there are going to be > a lot of questions about Gaussian. So let's tolerate such queries, when they > arise as a last resort. > Dear CCl users, I have been fallowing the discussion for several days on the Gaussian CCL users wondering how long it would take until someone would finally start "defending" the Gaussian users. Of course it could have been me... In agreement with what is on top I would just like to add part of my own experience to it. I am not a long time CCL user, but what I appreciate the most since I am linked to it is the diversity of the subjects, including Gaussian. I am myself a Gaussian user but not only, and a compilation problem with Gaussian was the main reason of my CCL subscription. It was more then 6 month ago when I had asked at Gaussian-help how I could compile on a new HP-processor and system. The only answer I recieved was that they were working on it and that they would contact me as soon as possible. They are still working on it, that is what they answered me when I had submited my question on CCL. But one day after I had resolved my compilation problem with the help of the CCL Gaussian users. I do agree that sometimes the questions could be solved by having a better look to the manuals, but this is not particular to Gaussian, one can also observe it for other software. I also consider that if I do not want to "loose" time reading message which I am not interested in I just delate it after reading its subject. CCL is a general talking field, I think one must tolerate every one if we want to keep its interest. Science is also a question of attention, maybe even to tolerence Thanks to your own attention, hopping I did not make you loose to much of your precious time. Laurent Troxler ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@/\@@/\@@/\@@@@ Laurent TROXLER / \/ \/ \ Lab. Modelisation et Simulations Moleculaires / /\/ /\/ /\ \ Universite Louis Pasteur \ \/ /\/ /\/ / 4, rue Blaise Pascal \ \/\ \/\ \/ 67070 Strasbourg (France) /\ \/\ \/\ \ E-mail: troxler@crypt.u-strasbg.fr / /\/ /\/ /\ \ Tel : (33) 3 88 41 62 87 \ \/ /\/ /\/ / @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\@@/\@@/\@@/@@@ """"""""""""""""""""""""""""""""""""""""""""""""""\/""\/""\/"""" From CAVALLO@CHEMNA.DICHI.UNINA.IT Mon May 26 04:44:48 1997 Received: from CHEMNA.DICHI.UNINA.IT for CAVALLO@CHEMNA.DICHI.UNINA.IT by www.ccl.net (8.8.3/950822.1) id DAA02416; Mon, 26 May 1997 03:49:13 -0400 (EDT) From: Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V5.0-6 #15194) id <01IJBKI4J39C000803@CHEMNA.DICHI.UNINA.IT> for CHEMISTRY@www.ccl.net; Mon, 26 May 1997 09:49:05 +0100 (CET) Date: Mon, 26 May 1997 09:47:06 +0100 (CET) Subject: Droplet area & gyration radius To: CHEMISTRY@www.ccl.net Message-id: <01IJBKMAR0TW000803@CHEMNA.DICHI.UNINA.IT> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, I have been told that for a droplet the following formula holds: ln (SASA/N) scales as -G/3 where: SASA = solvent accesible surface area N = Numbers of atoms G = Radius of gyration I looked for references, but no luck. Any hint ? Thanx Luigi -------------------------------------------------------------------------------- | Dr. Luigi Cavallo | | Department Of Chemistry Fax : ++39-81-5527771 | | University Of Naples Ph : ++39-81-5476535 | | Via Mezzocannone 4 Email : cavallo@chemna.dichi.unina.it | | I-80134 Naples, ITALY | -------------------------------------------------------------------------------- From m.schoonman@organon.akzonobel.nl Mon May 26 06:44:49 1997 Received: from gatekeeper.oss.akzonobel.nl for m.schoonman@organon.akzonobel.nl by www.ccl.net (8.8.3/950822.1) id GAA03045; Mon, 26 May 1997 06:31:00 -0400 (EDT) Received: (from mail@localhost) by gatekeeper.oss.akzonobel.nl (8.7.5/8.7.3) id MAA32540 for ; Mon, 26 May 1997 12:39:16 +0200 (MET DST) Received: from apou01.akzonobel.nl(145.49.90.59) by gatekeeper.oss.akzonobel.nl via smap (V2.0alpha) id xma029459; Mon, 26 May 97 12:38:50 +0200 Received: by apou01.akzonobel.nl id MAA31790; Mon, 26 May 1997 12:33:02 +0200 (MET DST) Received: (from schoonman@localhost) by organon.akzonobel.nl (950413.SGI.8.6.12/8.6.12) id KAA21041 for chemistry@www.ccl.net; Mon, 26 May 1997 10:32:17 GMT From: "schoonman Account" Message-Id: <9705261232.ZM21039@violet.oss.akzonobel.nl> Date: Mon, 26 May 1997 12:32:17 +0000 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Summary THREADING PROGRAMS Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19705261232.ZM21039.oss.akzonobel.nl" -- --PART-BOUNDARY=.19705261232.ZM21039.oss.akzonobel.nl Content-Type: text/plain; charset=us-ascii Summary THREADING PROGRAMS ______________________________________________________________________ * Threader 2 (released May 14th 1997) (downloadable): http://globin.bio.warwick.ac.uk/~jones/threader.html * 123D (server): http://www-lmmb.ncifcrf.gov/~nicka/run123D.html * Match-Box Web Server (server): http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html * ProFIT - Protein Fold Identification Tool: (threading based on an empirical "energy" function) For information: http://lore.came.sbg.ac.at/Extern/software/Profit/profit.html For the program: ftp: "gundi.came.sbg.ac.at" * Threading by Recursive Dynamic Programming [RDP]and Easy ToPLign Fold Prediction (servers): http://cartan.gmd.de/ToPLign.html * 123D TopLign : threading tool based on secondary structure prediction and residue-residue contact potential (part of the GMD-SCAI server), Zimmer group http://cartan.gmd.de/123D-test.html REF: N.N. Alexandrov, R. Nussinov and R.M. Zimmer Fast protein fold recognition via sequence to structure alignment and contact capacity potentials Pacific Symposium on Biocomputing '96 (Lawrence Hunter & Teri E. Klein, Eds) World Scientific Publishing Co., Singapore, pp. 53-72 * Gon+predss / Gon+predss+MULT : (part of the UCLA-DOE frsvr server) Fischer threading approach, considers predicted secondary structure in addition to fold recognition, Eisenberg group http://www.mbi.ucla.edu/people/frsvr/frsvr.html REF: D. Fischer and D. Eisenberg Fold recognition using sequence-derived predictions. Protein Science 5:947-955 (1996) * H3P2 : Rice threading approach (part of the UCLA-DOE frsvr server), considers predicted secondary structure, Eisenberg group http://www.mbi.ucla.edu/people/frsvr/frsvr.html REF: D. Rice and D. Eisenberg A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence J.Mol.Biol. submitted (1996) * RDP : threading by recursive dynamic programming (part of the GMD-SCAI server), Lengauer group http://cartan.gmd.de/cgi-bin/ToPLignLogin?/home/protal/WWW+/home/protal/ WWW/fast+FastLogin.rc+FastRDP REF: R. Thiele, R. Zimmer and T. Lengauer Recursive dynamic programming for adaptive sequence and structure alignment Ismb 3:384-92 (1995) * TOPITS (called PHDthreader as part of the PredictProtein server) : threading based on secondary structure prediction and solvent accessibility prediction, Burkhard Rost http://www.embl-heidelberg.de/predictprotein/ REF: B. Rost TOPITS: threading one-dimensional predictions into three-dimensional structures Ismb 3:314-321 (1995) * The PSCAN server Page: http://www.biokemi.su.se/~threader_server/pscan/ * Swiss-Model (M.Peitsch) (server): http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html =========================================== Replies from and thanks to: -> gerloff@cmpharm.ucsf.edu -> Gerald.Loeffler@univie.ac.at -> Roman.Efremov@univ-lille1.fr -> Ralf.Zimmer@gmd.de -> sangeeta@bioinfo.ernet.in -> gunnj@CERCA.UMontreal.CA -> rwoods@mailhost.tcs.tulane.edu -> stoutepf@carbon.dmpc.com -> m.dooley@mailbox.uq.edu.au -> arne@rune.biokemi.su.se -> Herrmann@informatik.uni-stuttgart.de =========================================== -- ___________________________________________________________________ Marten J.L. Schoonman Organon N.V. RK2340 m.schoonman@organon.akzonobel.nl P.O.Box 20 tel 0412-661469 daytime 5340 BH OSS 0317-423088(4) evening The Netherlands ___________________________________________________________________ --PART-BOUNDARY=.19705261232.ZM21039.oss.akzonobel.nl X-Zm-Content-Name: threader_sites.txt Content-Description: Text Content-Type: text/plain ; name="threader_sites.txt" ; charset=us-ascii Summary THREADING PROGRAMS ______________________________________________________________________ * Threader 2 (released May 14th 1997) (downloadable): http://globin.bio.warwick.ac.uk/~jones/threader.html * 123D (server): http://www-lmmb.ncifcrf.gov/~nicka/run123D.html * Match-Box Web Server (server): http://www.fundp.ac.be/sciences/biologie/bms/matchbox_submit.html * ProFIT - Protein Fold Identification Tool: (threading based on an empirical "energy" function) For information: http://lore.came.sbg.ac.at/Extern/software/Profit/profit.html For the program: ftp: "gundi.came.sbg.ac.at" * Threading by Recursive Dynamic Programming [RDP]and Easy ToPLign Fold Prediction (servers): http://cartan.gmd.de/ToPLign.html * 123D TopLign : threading tool based on secondary structure prediction and residue-residue contact potential (part of the GMD-SCAI server), Zimmer group http://cartan.gmd.de/123D-test.html REF: N.N. Alexandrov, R. Nussinov and R.M. Zimmer Fast protein fold recognition via sequence to structure alignment and contact capacity potentials Pacific Symposium on Biocomputing '96 (Lawrence Hunter & Teri E. Klein, Eds) World Scientific Publishing Co., Singapore, pp. 53-72 * Gon+predss / Gon+predss+MULT : (part of the UCLA-DOE frsvr server) Fischer threading approach, considers predicted secondary structure in addition to fold recognition, Eisenberg group http://www.mbi.ucla.edu/people/frsvr/frsvr.html REF: D. Fischer and D. Eisenberg Fold recognition using sequence-derived predictions. Protein Science 5:947-955 (1996) * H3P2 : Rice threading approach (part of the UCLA-DOE frsvr server), considers predicted secondary structure, Eisenberg group http://www.mbi.ucla.edu/people/frsvr/frsvr.html REF: D. Rice and D. Eisenberg A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence J.Mol.Biol. submitted (1996) * RDP : threading by recursive dynamic programming (part of the GMD-SCAI server), Lengauer group http://cartan.gmd.de/cgi-bin/ToPLignLogin?/home/protal/WWW+/home/protal/ WWW/fast+FastLogin.rc+FastRDP REF: R. Thiele, R. Zimmer and T. Lengauer Recursive dynamic programming for adaptive sequence and structure alignment Ismb 3:384-92 (1995) * TOPITS (called PHDthreader as part of the PredictProtein server) : threading based on secondary structure prediction and solvent accessibility prediction, Burkhard Rost http://www.embl-heidelberg.de/predictprotein/ REF: B. Rost TOPITS: threading one-dimensional predictions into three-dimensional structures Ismb 3:314-321 (1995) * The PSCAN server Page: http://www.biokemi.su.se/~threader_server/pscan/ * Swiss-Model (M.Peitsch) (server): http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html =========================================== Replies from and thanks to: -> gerloff@cmpharm.ucsf.edu -> Gerald.Loeffler@univie.ac.at -> Roman.Efremov@univ-lille1.fr -> Ralf.Zimmer@gmd.de -> sangeeta@bioinfo.ernet.in -> gunnj@CERCA.UMontreal.CA -> rwoods@mailhost.tcs.tulane.edu -> stoutepf@carbon.dmpc.com -> m.dooley@mailbox.uq.edu.au -> arne@rune.biokemi.su.se -> Herrmann@informatik.uni-stuttgart.de =========================================== --PART-BOUNDARY=.19705261232.ZM21039.oss.akzonobel.nl-- From m.schoonman@organon.akzonobel.nl Mon May 26 08:44:50 1997 Received: from gatekeeper.oss.akzonobel.nl for m.schoonman@organon.akzonobel.nl by www.ccl.net (8.8.3/950822.1) id HAA03391; Mon, 26 May 1997 07:53:22 -0400 (EDT) Received: (from mail@localhost) by gatekeeper.oss.akzonobel.nl (8.7.5/8.7.3) id OAA16881 for ; Mon, 26 May 1997 14:01:34 +0200 (MET DST) Received: from apou01.akzonobel.nl(145.49.90.59) by gatekeeper.oss.akzonobel.nl via smap (V2.0alpha) id xma016109; Mon, 26 May 97 14:00:08 +0200 Received: by apou01.akzonobel.nl id NAA32220; Mon, 26 May 1997 13:54:20 +0200 (MET DST) Received: (from schoonman@localhost) by organon.akzonobel.nl (950413.SGI.8.6.12/8.6.12) id LAA21119 for chemistry@www.ccl.net; Mon, 26 May 1997 11:53:34 GMT From: "schoonman Account" Message-Id: <9705261353.ZM21117@violet.oss.akzonobel.nl> Date: Mon, 26 May 1997 13:53:32 +0000 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Threading: 0% holomogy? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Can someone tell me, which PDB-available structures have similar structures but no (or hardy any) sequence identity? Thank you in advance! ___________________________________________________________________ Marten J.L. Schoonman Organon N.V. RK2340 m.schoonman@organon.akzonobel.nl P.O.Box 20 tel 0412-661469 5340 BH OSS, The Netherlands -- ___________________________________________________________________ Marten J.L. Schoonman Organon N.V. RK2340 m.schoonman@organon.akzonobel.nl P.O.Box 20 tel 0412-661469 daytime 5340 BH OSS 0317-423088(4) evening The Netherlands ___________________________________________________________________ From churca@opium.q1.fcen.uba.ar Mon May 26 11:44:51 1997 Received: from opium.q1.fcen.uba.ar for churca@opium.q1.fcen.uba.ar by www.ccl.net (8.8.3/950822.1) id KAA04196; Mon, 26 May 1997 10:59:03 -0400 (EDT) Received: from localhost (churca@localhost) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id LAA12351; Mon, 26 May 1997 11:52:22 -0300 Date: Mon, 26 May 1997 11:52:22 -0300 (ARST) From: Ojitos To: "Marc-A. Houle" cc: chemistry@www.ccl.net Subject: Re: CCL:Next Edition of the Journal of the Chemical Computing Group In-Reply-To: <1.5.4.16.19970513150417.40276ff6@mail.chemcomp.com> Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="1553798431-27277605-864658342=:12284" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --1553798431-27277605-864658342=:12284 Content-Type: TEXT/PLAIN; charset=US-ASCII Adrian Turjanski churca@q1.fcen.uba.ar --1553798431-27277605-864658342=:12284 Content-Type: TEXT/PLAIN; charset=US-ASCII; name=tt Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: information about MOE DQpIaSwgbXkgbmFtZSBpcyBBZHJpYW4gVHVyamFuc2tpIGFuZCBpJ20gaW50 ZXJlc3RlZCBpbiBNT0UuIENhbiB5b3UgdGVsbCBtZQ0KaG93IGNhbiBpIGdl dCB0byB3b3JrIHdpdGggaXQuIEknbSB3b3JraW5nIGF0IHRoZSBCdWVub3Mg QWlyZXMgVW5pdmVyc2l0eSBpbg0KdGhlIE1vbGVjdWxhciBNb2RlbGluZyBn cm91cC4NCg0KDQogICAgICAgICAgICAgICAgICAgICAgICBUaGFua3MgDQog ICAgICAgICAgICAgICAgICAgICAgICAgQWRyaWFuIFR1cmphbnNraQ0KICAg ICAgICAgICAgICAgICAgICAgICAgIGNodXJjYUBxMS5mY2VuLnViYS5hcg0K DQo= --1553798431-27277605-864658342=:12284-- From churca@opium.q1.fcen.uba.ar Mon May 26 15:44:53 1997 Received: from opium.q1.fcen.uba.ar for churca@opium.q1.fcen.uba.ar by www.ccl.net (8.8.3/950822.1) id OAA04984; Mon, 26 May 1997 14:56:11 -0400 (EDT) Received: from localhost (churca@localhost) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id PAA13794; Mon, 26 May 1997 15:49:27 -0300 Date: Mon, 26 May 1997 15:49:26 -0300 (ARST) From: Ojitos To: Eugene Leitl cc: chemistry@www.ccl.net Subject: Re: CCL:G:I'm sorry In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I didn't realize that the mail couldn't be read.I didn't write that the test was written in MIME format, the program pine did it, It was a mistake. I apologize for the problems, i hope i can send a new mail that everybody can read. In the other mail i wanted to know how can i get MOE and SVL. If i have to buy or not. I work at the Buenos Aires university. Adrian Turjanski churca@q1.fcen.uba.ar