From val@nmr1.ioc.ac.ru Sun Dec 22 03:11:15 1996 Received: from nmr1.ioc.ac.ru for val@nmr1.ioc.ac.ru by www.ccl.net (8.8.3/950822.1) id CAA15995; Sun, 22 Dec 1996 02:29:11 -0500 (EST) Received: from [193.233.3.213] (nmr-v.ioc.ac.ru [193.233.3.213]) by nmr1.ioc.ac.ru (8.6.12/8.6.9) with SMTP id KAA27856 for ; Sun, 22 Dec 1996 10:29:28 +0300 Date: Sun, 22 Dec 96 10:27:04 +0300 From: "Ananikov V.P." Message-Id: <50921.val@nmr1.ioc.ac.ru> X-Minuet-Version: Minuet1.0_Beta_17A Reply-To: X-POPMail-Charset: IBM 8-Bit To: chemistry@www.ccl.net Subject: Re: NMR prediction On Wed, 18 Dec 1996 08:54:32 +0100 (MET), Gianluca Sbardella wrote: > > >Dear colleagues, >I'm looking for a good program (freeware) for the prediction of NMR >spectra of given structures.Can anybody help me? >Any reference (ftp sites or eveything else..) would be appreciated. >Thank you a lot in advance, > >Gianluca Sbardella > Dear Dr. Gianluca, If you are looking for nmr software a good point to start is NMR Software List prepared by P.Lundberg (Peter.Lundberg@chem.umu.se) available at: http://www.chem.umu.se/divisions/fk/EduNMRSoft.html For practical purpose, it is good to begining with the programs calculating chemical shift with additivity relationships, usually they are simple and easy to use. I think there is no freeware in this class of programs because of for increasing accuracy a very large data base with experimental chemical shifts is needed. You can try ACD/CNMR for 13C and ACD/HNMR for 1H chemical shift prediction. ACD/CNMR v1.0, 1995 uses an internal data base with over than 120,000 experimental chemical shifts and calculates 13C NMR spectra for almost any drawn structure. Demos are available at: http://www.acdlabs.com The people interesting in additional information about ACD Inc. products may subscribe to ACDLabs_prog mailing list. To receive more info send an e-mail with HELP in the body of the letter to: ACDLabs_prog-Request@nmr1.ioc.ac.ru (some authors of ACD/NMR package are subscribed to this list). Happy new year! best wishes, Valentin. Valentin P. Ananikov (Post-Graduate Student) NMR Laboratory N.D. Zelinsky Institute of Organic Chemistry Leninsky Prospect 47 Moscow 117913 Russia e-mail: val@nmr1.ioc.ac.ru Fax (095) 135 5328 Phone (095) 135 9094, (095) 938 3536 From ccl@www.ccl.net Sun Dec 22 06:11:15 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id FAA16207; Sun, 22 Dec 1996 05:14:36 -0500 (EST) Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by bedrock.ccl.net (8.8.3/950822.1) id FAA18318; Sun, 22 Dec 1996 05:14:34 -0500 (EST) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id LAA20216; Sun, 22 Dec 1996 11:15:44 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.4/8.8.4) id LAA07304; Sun, 22 Dec 1996 11:13:37 +0100 Date: Sun, 22 Dec 1996 11:13:37 +0100 Message-Id: <199612221013.LAA07304@lmspc1.ibs.fr> From: Konrad Hinsen To: raeker@saturn.kent.edu CC: chemistry@ccl.net In-reply-to: (raeker@saturn.kent.edu) Subject: Re: CCL:CCL: Sample OpenGL code for Molecular Display. > Does anyone have sample OpenGL code for 3D display of molecules > (stick, ball and stick, or CPK) that they would be willing to share. I > am working on a GUI for some of my programs and would like to include > display of molecules and density surfaces. I can do the coding An alternative you could consider is using VRML. VRML code is easy to produce, and there are a number of VRML browsers available for free. I do have some VRML producing code (written in Python), including support for wireframe and all-and-stick models for molecules, in case anyone is interested. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From ccl@www.ccl.net Tue Dec 24 01:11:39 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id AAA26108; Tue, 24 Dec 1996 00:58:32 -0500 (EST) Received: from badoit.chem.nagoya-u.ac.jp for mito@badoit.chem.nagoya-u.ac.jp by bedrock.ccl.net (8.8.3/950822.1) id AAA05988; Tue, 24 Dec 1996 00:58:11 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by badoit.chem.nagoya-u.ac.jp (8.6.12/8.6.12) with SMTP id FAA11506; Tue, 24 Dec 1996 05:53:12 GMT Message-Id: <199612240553.FAA11506@badoit.chem.nagoya-u.ac.jp> X-Authentication-Warning: badoit.chem.nagoya-u.ac.jp: Host localhost didn't use HELO protocol To: "Todd J. Raeker" CC: chemistry@ccl.net Reply-to: mito@aqua.chem.nagoya-u.ac.jp Subject: Re: Sample OpenGL code for Molecular Display. In-reply-to: Your message of "Wed, 18 Dec 1996 11:00:23 EST." Date: Tue, 24 Dec 1996 14:53:11 +0900 From: Masakatsu Ito > Does anyone have sample OpenGL code for 3D display of molecules > (stick, ball and stick, or CPK) that they would be willing to share. I I've been employing vtk (the Visualization Toolkit) to develope the program for visualizing my MD calculations. Vtk is a C++ class libraray. The renderer libraries that vtk supports are Sun's XGL, SGI's GL and OpenGL, HP's starbase and the Mesa OpenGL renderer which should work on most machines that have X-windows. The home page of vtk is, http://www.cs.rpi.edu/~martink/ Masakatsu Ito Department of Structual Molecular Science The Graduate University for Advanced Studies Tel 81(Japan)-52-789-3656 Fax 81(Japan)-52-789-3551 E-mail mito@aqua.chem.nagoya-u.ac.jp Web http://www.chem.nagoya-u.ac.jp/~mito/mitoEng.html From toukie@zui.unizh.ch Fri Dec 27 09:12:20 1996 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id IAA15610; Fri, 27 Dec 1996 08:35:49 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA14549; Fri, 27 Dec 1996 14:40:47 +0100 Message-Id: <1.5.4.32.19961227133702.00665288@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 Dec 1996 14:37:02 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Seeking .wrl converter Cc: chminf-l@iubvm.ucs.indiana.edu Dear Colleagues; I am seeking a utility compatible with Windows 95 that will enable me to take a chemical structure saved in one of the common chemical structure formats (.ent, .mol2, etc.) and convert it to a virtual reality .wrl file so that I may view it using the "live3d" plug-in that accompanies Netscape 3.0. If you can help me, kindly contact me _directly_ at toukie@zui.unizh.ch Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-8028 ZH 7 toukie@zui.unizh.ch From ccluser@chu.chem.nthu.edu.tw Fri Dec 27 10:25:29 1996 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.8.3/950822.1) id JAA15774; Fri, 27 Dec 1996 09:39:29 -0500 (EST) From: Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA21351; Fri, 27 Dec 1996 21:30:10 +0800 Message-Id: <9612271330.AA21351@chu.chem.nthu.edu.tw> Subject: BH&HLYP in G94? To: CHEMISTRY@www.ccl.net Date: Fri, 27 Dec 96 21:30:09 TAIST X-Mailer: ELM [version 2.4dev PL17] Dear all, I tried to use the functional BH&HLYP of DFT in G94, but it did not work. And I saw the explaination of this functional in G94.OLD/bsd/l1.hlp. So, I think it must have something wrong in my input file. Please check for me. Any reply will be appreciate! The followings are the input and output file I got, input: 1 $rungaussian 2 %chk=hcooh-h2-ts-dft-bh 3 #n bhandhlyp/6-31g** scf=direct optcyc=5 4 scfcyc=100 opt=(ts,noeigen,z-matrix) test 5 6 -------hcooh-h2-ts-dft-bh------- 7 8 0 1 9 C 10 O 1 r1 11 O 1 r2 2 a1 12 H 1 r3 3 a2 2 d1 13 H 3 r4 1 a3 4 d2 14 15 r1=1.1760 16 r2=1.2600 17 r3=1.4470 d 18 r4=1.3079 d 19 a1=147.0 20 a2=99.16 21 a3=68.33 22 d1=180.0 23 d2=0.0 output: Gaussian 94: IBM-RS6000-G94RevB.1 16-Apr-1995 27-Dec-1996 ********************************************** %chk=hcooh-h2-ts-dft-bh ---------------------------------------------------------------------- #n bhandhlyp/6-31g** scf=direct optcyc=5 scfcyc=100 opt=(ts,noeigen,z-matrix) test ---------------------------------------------------------------------- QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. #N BHANDHLYP/6-31G** SCF=DIRECT OPTCYC=5 SC ' Last state="GCL" TCursr= 2897 LCursr= 3 Error termination via Lnk1e in /Exp/proj/p002/g94/l1.exe. Job cpu time: 0 days 0 hours 0 minutes .1 seconds. File lengths (MBytes): RWF= 1 Int= 0 D2E= 0 Chk= 1 Scr= 1 bsh: 12730 Memory fault: A memory image file is created as "core". ===================================================================== Chiu-Ling Lin | E-mail: lin@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From unipune.ernet.in!gadre@iucaa.ernet.in Fri Dec 27 14:12:23 1996 Received: from sangam.ncst.ernet.in for unipune.ernet.in!gadre@iucaa.ernet.in by www.ccl.net (8.8.3/950822.1) id NAA16687; Fri, 27 Dec 1996 13:48:30 -0500 (EST) Received: (from root@localhost) by sangam.ncst.ernet.in (8.7.5) id AAA17843 for CHEMISTRY@www.ccl.net; Sat, 28 Dec 1996 00:22:31 +0530 (GMT+05:30) >Received: from unipune.ernet.in by iucaa (4.1/SMI-4.1) id AA06269; Fri, 27 Dec 96 09:59:19+050 Received: from iucaa by sangam.ncst.ernet.in; Sat, 28 Dec 1996 00:22 GMT Received: from unipune.ernet.in by iucaa (4.1/SMI-4.1) id AA06269; Fri, 27 Dec 96 09:59:19+050 Received: by unipune.ernet.in (5.0/SMI-SVR4.1.0) id AA11318; Fri, 27 Dec 1996 09:54:26 +0500 Date: Fri, 27 Dec 1996 09:54:26 +0500 From: gadre@unipune.ernet.in (Faculty) Message-Id: <9612271454.AA11318@unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Ion pairs Cc: gadre@unipune.ernet.in Content-Type: text Dear Sirs: We have recently developed a topography based technique (simple but elegant) for studying ion-pair formation. The system can be organic, inorganic or biological. We would like to test it on some real-life problems. Potential collaborators are welcome to write to us. Thanks...........................Shridhar R. Gadre From bruno@antas.agraria.uniss.it Sun Dec 29 13:12:48 1996 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id MAA24633; Sun, 29 Dec 1996 12:32:29 -0500 (EST) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA269050803; Sun, 29 Dec 1996 18:33:23 +0100 Sender: bruno@antas.agraria.uniss.it Message-Id: <32C6AB63.41C6@antas.agraria.uniss.it> Date: Sun, 29 Dec 1996 18:33:23 +0100 From: bruno Organization: DISAABA University of Sassari X-Mailer: Mozilla 3.0Gold (X11; I; AIX 2) Mime-Version: 1.0 To: "Hr. Dr. S. Shapiro" Cc: chemistry@www.ccl.net Subject: Re: CCL:Seeking .wrl converter References: <1.5.4.32.19961227133702.00665288@zui.unizh.ch> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hr. Dr. S. Shapiro wrote: > > Dear Colleagues; > > I am seeking a utility compatible with Windows 95 that will enable me > to take a chemical structure saved in one of the common chemical structure > formats (.ent, .mol2, etc.) and convert it to a virtual reality .wrl file > so that I may view it using the "live3d" plug-in that accompanies Netscape > 3.0. If you can help me, kindly contact me _directly_ at > > toukie@zui.unizh.ch > > Thanks in advance to all responders. > > Sincerely, > > (Dr.) S. Shapiro > Inst. f. orale Mikrobiol. u. allg. Immunol. > Zent. f. Zahn-, Mund- u. Kieferheilkd. der Univ. ZH > Plattenstr. 11 > Postfach > CH-8028 ZH 7 > > toukie@zui.unizh.ch try the pdb2vrml converter at this url: http://ws05.pc.chemie.th-darmstadt.de/vrml/pdb2vrml.html also the msi weblab viewer reads files in most of the common chemical formats and can output a wrl file. It is free for download at: http://www.msi.com/weblab/download.htm regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it