From chemistry-request@ccl.net Tue Oct 14 07:03:22 2003 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9EB2odH018156 for ; Tue, 14 Oct 2003 07:02:51 -0400 Received: from conversion_l.unisi.it by cuces.unisi.it (PMDF V6.2-X17 #30546) id <01L1TI3XJUDC000OJG/at/cuces.unisi.it> for chemistry/at/ccl.net; Tue, 14 Oct 2003 12:50:12 +0100 (MET) Received: from unisi.it (sgio2.ctf.unisi.it [172.16.52.81]) by cuces.unisi.it (PMDF V6.2-X17 #30546) with ESMTPA id <01L1THPYFZB8000QP6/at/cuces.unisi.it> for chemistry/at/ccl.net; Tue, 14 Oct 2003 12:27:24 +0100 (MET) Date: Tue, 14 Oct 2003 12:24:43 +0200 From: Stefano Forli Subject: AutoDock output file format Sender: stefano/at/student.unisi.it To: chemistry/at/ccl.net Message-id: <3F8BCEEB.235046D/at/unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=UTF-7 Content-transfer-encoding: 7bit X-Accept-Language: en X-Spam-Status: No, hits=-0.3 required=7.0 tests=SIGNATURE_LONG_DENSE,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, what is the best way to analyze the output structures of autodock jobs? I found some scripts (PDB_to_car.bcl and car2arc.awk) to convert pdb files in arc files for insightII, but it's unformatted so all lines are merged, and are unreadable. I even tried babel to make some conversion, but I don't know what is the best mix of formats to load protein and ligands (in our lab we have Macromodel too). Any suggestion will be appreciated... Thanks Stefano -- *********************************** Dr. Forli Stefano PhD Student Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 *********************************** From chemistry-request@ccl.net Mon Oct 13 19:06:31 2003 Received: from mhub-w2.tc.umn.edu (mhub-w2.tc.umn.edu [160.94.160.45]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9DN5xdH006593 for ; Mon, 13 Oct 2003 19:05:59 -0400 Received: from firefox.software.umn.edu (firefox.software.umn.edu [128.101.103.112]) by mhub-w2.tc.umn.edu with ESMTP for chemistry!at!ccl.net; Mon, 13 Oct 2003 18:05:53 -0500 (CDT) X-Umn-Remote-Mta: [N] firefox.software.umn.edu #+LO Received: (from nobody@localhost) by firefox.software.umn.edu (8.12.9/8.12.8) id h9DN5q8i018992; Mon, 13 Oct 2003 18:05:52 -0500 Message-Id: <200310132305.h9DN5q8i018992!at!firefox.software.umn.edu> Date: Mon, 13 Oct 2003 18:05:52 CDT From: Yan Zhao Subject: CBS-Q and CBS-APNO question To: chemistry!at!ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; CHARSET=US-ASCII X-Tick-Nemesis: American Maid X-remote-user-ip: 160.94.96.166 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) Hi, there Does anyone knows how to do single point calculation with CBS-B and CBS-APNO in Gaussian 03. In other word, how do we disable the optimization step in the CBS-B and CBS-APNO.The Iop does not work for those two case. Thanks *************************************** Yan Zhao yzhao!at!chem.umn.edu Smith Hall 334 (612)-626-2213 Department of Chemistry University of Minnesota 207 Pleasant St SE Minneapolis, MN 55455 *************************************** From chemistry-request@ccl.net Tue Oct 14 11:27:19 2003 Received: from ultra3000.if.sc.usp.br (ultra3000.if.sc.usp.br [143.107.228.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9EFQcdH025264 for ; Tue, 14 Oct 2003 11:26:40 -0400 Received: from if.sc.usp.br (floyd.if.sc.usp.br [143.107.228.51]) by ultra3000.if.sc.usp.br (8.11.6/8.11.0) with ESMTP id h9EFNpQ21021 for ; Tue, 14 Oct 2003 13:23:51 -0200 Message-ID: <3F8BEBC8.2020509*at*if.sc.usp.br> Date: Tue, 14 Oct 2003 12:27:52 +0000 From: Alexandre Suman de Araujo User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry*at*ccl.net Subject: Parameters for Cadmium Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit 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) Hi CLLers!!! I'm looking for LJ parameters for cadmium to use in simulations of the Cd ion in a solvent. Does somebody can help me??? Thank's a lot -- Alexandre Suman de Araujo asaraujo*at*if.sc.usp.br UIN: 6194055 IFSC - USP - Sco Carlos - Brasil From chemistry-request@ccl.net Tue Oct 14 13:49:19 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9EHmldH029779 for ; Tue, 14 Oct 2003 13:48:47 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.12.8/8.12.8/OSC 3.0) with ESMTP id h9EHmwIo012195 for ; Tue, 14 Oct 2003 13:48:58 -0400 Date: Tue, 14 Oct 2003 13:48:46 -0400 (EDT) From: "Dr. Jan K Labanowski" To: chemistry*at*ccl.net Subject: 2nd Industrial Fluids Properties Simulation Challenge Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ---------- Forwarded message ---------- Date: Wed, 24 Sep 2003 15:07:08 -0500 From: rbross*at*mmm.com To: jkl*at*ccl.net Topic: 2nd Industrial Fluids Properties Simulation Challenge It is with great pleasure we announce the Second Industrial Fluid Properties Simulation Challenge. The second challenge follows the successful conclusion of the first challenge which led to significant assessment and advancements of simulation methodology via the application to research challenge problems for prediction of vapor-liquid equilibria, density, and viscosity. The Second Simulation Challenge will focus on prediction of vapor pressures and heats of vaporization, gas solubility, and enthalpies of mixing for materials. For details on Second Simulation Challenge as well as on the results of the first competition and could you please see the attached announcement and/or http://www.cstl.nist.gov/FluidSimulationChallenge. The goal of the Industrial Fluid Properties Simulation Challenge (IFPSC) is to obtain an in-depth and objective assessment of our current abilities and inabilities in the prediction of physical properties for industrially challenging fluids. The accuracy of property prediction is based on the choice of forcefield and modeling technique. As a result, it is anticipated that the awardees of each problem in this competition will develop or apply an accurate and general forcefield that can model a range of different chemistries and develop or apply a modeling technique that can handle materials in different states (liquid/vapor), is precise and accurate, and computationally swift. Industrial and NIST Organizing Committee From chemistry-request@ccl.net Tue Oct 14 13:01:36 2003 Received: from mxout6.cac.washington.edu (mxout6.cac.washington.edu [140.142.33.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9EH14dH028599 for ; Tue, 14 Oct 2003 13:01:04 -0400 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout6.cac.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h9EH130Y010760 for ; Tue, 14 Oct 2003 10:01:03 -0700 Received: from u.washington.edu (D-128-95-235-174.dhcp4.washington.edu [128.95.235.174]) (authenticated bits=0) by smtp.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h9EH12SR002183 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Tue, 14 Oct 2003 10:01:02 -0700 Message-ID: <3F8C2BCE.60101*at*u.washington.edu> Date: Tue, 14 Oct 2003 10:01:02 -0700 From: Oliver Hucke User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry*at*ccl.net Subject: RESI charmm top entry for HETATM pdb residues 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, recently I posted a question on the generation on RESI entries in the CHARMM topology file for HETATM residues in a pdb structure. Thanks to Richard Wood, Liisa Iaakkonen and Giulio Vistoli for their replies! So far I was pointed to the program VEGA (http://www.ddl.unimi.it) which can produce the psf file for a pdb structure. Actually I am interested in the generation of the RESI entry in the topology library file of charmm. Especially: How should I derive the entries in the Internal coordinate section ("IC")? Any hints are very much appreciated! Best, Oliver -- _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific St Seattle, WA 98195 T:(206)685-7046 _______________________________________ From chemistry-request@ccl.net Tue Oct 14 21:22:04 2003 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9F1LXdH009300 for ; Tue, 14 Oct 2003 21:21:33 -0400 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id E0E5F7D39; Wed, 15 Oct 2003 03:21:32 +0200 (CEST) To: chemistry..at..ccl.net Subject: CUTOFF in GAMESS-US Message-ID: <1066180892.3f8ca11cd23a1..at..webmail.u-picardie.fr> Date: Wed, 15 Oct 2003 03:21:32 +0200 (CEST) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=1.2 required=7.0 tests=UPPERCASE_25_50,USER_AGENT version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, In the GAMESS-US ouput, one can see such information printed: ------------------------------- INTEGRAL TRANSFORMATION OPTIONS ------------------------------- NWORD = 0 CUTOFF = 1.0E-09 MPTRAN = 0 DIRTRF = F AOINTS =DUP I would be interested in decreasing this CUTOFF value from 1.0E-09 to 1.0E-10. In the GAMESS documentation, this keyword is ONLY described for MP2 calculations. Is it possible to decrease this CUTOFF in HF calculations ? If yes How ? Thanks, Regrads, Francois From chemistry-request@ccl.net Tue Oct 14 16:28:02 2003 Received: from pilot04.cl.msu.edu (pilot04.cl.msu.edu [35.9.5.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9EKRVdH001995 for >ccl.net>; Tue, 14 Oct 2003 16:27:31 -0400 Received: from [35.12.16.183] (pm652-41.dialip.mich.net [35.12.16.193]) by pilot04.cl.msu.edu (8.11.6p2/8.10.2) with ESMTP id h9EKRT665226 for >ccl.net>; Tue, 14 Oct 2003 16:27:30 -0400 Mime-Version: 1.0 X-Sender: chieny<>pilot.msu.edu Message-Id: Date: Tue, 14 Oct 2003 16:25:19 -0400 To: CHEMISTRY<>ccl.net From: Yao-Ying Chien >msu.edu> Subject: CCL: meaning of Ph.D.? Content-Type: text/plain; charset="us-ascii" X-Spam-Status: No, hits=0.5 required=7.0 tests=SATISFACTION version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, My 10 years old nephew asked me: "what is the meaning of Ph.D.?" I told him that Ph stands for Philosophy, and D is Doctor. He then asked me the meanings of philosophy and doctor? I was speechless and had to admit that I don't know. So please help me out or I cannot face him again ;=p 1. So far I know that phil = love; sophy = wisdom. Hence, philosophy = love wisdom. OK, I sort of know what love is (do I?), but how do I explain wisdom? Isn't it like a cycle: B explains A, C explains B, then suddenly A explains C? Namely, A <-- B <-- C <-- A. I am not satisfied with the explanation in most of the dictionaries or Encyclopedia. My nephew can easily make me speechless again. 2. What does Doctor mean? Compare and contrast with Master (as in MS or MA), and Bachelor (as in BS or BA). 3. Ooops! Troubles. He is going to ask me the meaning of Science, vs Art or Philosophy. See #4. 4. Does AD (or DA, Doctor of Art) exist? If we follow the format of MS = master of Science, MA = master of Art, then PhD (= Doctor of Philosophy) should be DPh. See the following pattern, BS BA MS MA DPh in Science, Engineer, etc. Where is Art? Pointers to URLs or books are appreciated, as long as it can make me face him confidently next time ;=) -- Regards, Yao-Ying Chien Department of Crop and Soil Sciences Michigan State University Plant and Soil Sciences Building, Rm A526 East Lansing, MI 48824-1325 Office: (517)355-9284 Fax: (517)355-0270 email: chieny<>pilot.msu.edu From chemistry-request@ccl.net Tue Oct 14 20:50:59 2003 Received: from mail.shcnc.ac.cn (server.shcnc.ac.cn [159.226.128.1]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9F0oPdH008739 for >ccl.net>; Tue, 14 Oct 2003 20:50:26 -0400 Received: from DATA4 (unknown [202.127.19.76]) by mail.shcnc.ac.cn (4U Message Server) with SMTP id EF08C416DB for >ccl.net>; Wed, 15 Oct 2003 08:48:21 +0800 (CST) Message-ID: <000e01c392b6$4cbec620$4c137fca<>simm.ac.cn> Reply-To: "Mingyue Zheng" >mail.shcnc.ac.cn> From: "Mingyue Zheng" >mail.shcnc.ac.cn> To: >ccl.net> Subject: ADME database Date: Wed, 15 Oct 2003 08:50:16 +0800 Organization: SIMM MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Spam-Status: No, hits=3.0 required=7.0 tests=BASE64_ENC_TEXT,RCVD_IN_RFCI version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h9F0oxdH008748 Hi all: Could anyone tell me where can I find ADME profiles of some kown drugs or compouds, for example ADME database or libaray or something like that. Thanks! (UTF-8) *********************************************************************** Mingyue Zheng Drug Design & Discovery Center SIMM,China Acadmy of Science 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park,Shanghai 201203,China Tel: 86-21-50806600 Fax: 86-21-50807088 myzheng<>mail.shcnc.ac.cn myzheng<>iris3.simm.ac.cn *********************************************************************** From chemistry-request@ccl.net Tue Oct 14 23:26:01 2003 Received: from polaris.scs.uiuc.edu (polaris.scs.uiuc.edu [130.126.231.226]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9F3PUdH012699 for ; Tue, 14 Oct 2003 23:25:30 -0400 Received: from scs.uiuc.edu (polaris.scs.uiuc.edu [130.126.231.226]) by polaris.scs.uiuc.edu (8.12.10/8.12.10) with SMTP id h9F3PUKe6095971; Tue, 14 Oct 2003 22:25:30 -0500 (CDT) From: Jerome Baudry Received: from 12.221.67.240 (SquirrelMail authenticated user jerome) by www.scs.uiuc.edu with HTTP; Tue, 14 Oct 2003 22:25:30 -0500 (CDT) Message-ID: <1230.12.221.67.240.1066188330.squirrel$at$www.scs.uiuc.edu> Date: Tue, 14 Oct 2003 22:25:30 -0500 (CDT) Subject: Re: CCL:meaning of Ph.D.? To: In-Reply-To: References: X-Priority: 3 Importance: Normal X-MSMail-Priority: Normal Cc: X-Mailer: SquirrelMail (version 1.2.7) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-0.9 required=7.0 tests=IN_REP_TO,MISSING_MIMEOLE,MISSING_OUTLOOK_NAME, QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > > 2. What does Doctor mean? Compare and contrast with Master (as in MS or > MA), and Bachelor (as in BS or BA). > 4. Does AD (or DA, Doctor of Art) exist? > If we follow the format of MS = master of Science, MA = master of Art, > then PhD (= Doctor of Philosophy) should be DPh. See the following > pattern, BS, BA, MS, MA > DPh in Science, Engineer, etc. Where is Art? These titles are from Latin, not English: "Doctor": capable of teaching, from "docere": to teach BA: "Baccalaureus Artium," MA: "Magister Artium," BS: "Baccalaureus Scientiae," MD: "Medicinae Doctor," Ph.D: "Philosophia Doctor" Salvate omnes, Hieronymus Baudry ;-) ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome$at$scs.uiuc.edu