From chemistry-request@server.ccl.net Tue Nov 6 09:12:24 2001 Received: from dalton.iq.ufrgs.br ([143.54.38.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6ECNB10036 for ; Tue, 6 Nov 2001 09:12:23 -0500 Received: by dalton.iq.ufrgs.br (Postfix, from userid 548) id 7AADE560FE; Tue, 6 Nov 2001 12:15:34 -0200 (BRST) Received: from localhost (localhost [127.0.0.1]) by dalton.iq.ufrgs.br (Postfix) with ESMTP id 69C6D560FC for ; Tue, 6 Nov 2001 12:15:34 -0200 (BRST) Date: Tue, 6 Nov 2001 12:15:34 -0200 (BRST) From: Jones de Andrade To: Subject: six-ligands problem in tinker? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all. I'm using the tinker package to make some calculations on some organometalic-complexes, specially doing calculations on its structure minimization and the normal mode analysis (for then make comparsions with the experiment). While I was using it for trigonal and/or tetraedral-like complexes, there was no problem. Now, I'm trying to make it work with some octaedral complexes (d2sp3), and the programs are giving me some errors. The message that it gives to me is: READXYZ -- Check Connection of Atom 1 to Atom 6 TINKER is Unable to Continue; Terminating the Current Calculation It appears to be a problem in the molecule definition (the tests that I have performed shows that the system arrive at this error *before* looking into the parameters file), but I've already looked into that too many times, and there seems to be ok. I've done that molecular input based on the other tetraedral inputs that I have and had already been tested. Without any other option to think about, I decided to ask the list for any help. I'm already thanking too much all the list for any time spended with this question. Thanks too for any help or suggestion on this subject. Without nothing more to say, except apologize for taking so much of all's time, Sincerally yours, Jones de Andrade *********************************************************** * Jones de Andrade * *********************************************************** * Theoretical Chemistry Group * Grupo de Quimica Teorica * * http://www.iq.ufrgs.br/theochem.html * * Institute of Chemistry * Instituto de Quimica * * http://www.iq.ufrgs.br/ * * Universidade Federal do Rio Grande do Sul * * http://www.ufrgs.br/ * * Brasil * *********************************************************** * E-mail:johannes@iq.ufrgs.br * * ICQ UIN: 17929775 * *********************************************************** * "We turn molecules into numbers, * * and numbers into molecules..." * *********************************************************** From chemistry-request@server.ccl.net Tue Nov 6 10:04:00 2001 Received: from francois.inserm.fr ([193.55.59.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6F3wB11341 for ; Tue, 6 Nov 2001 10:03:59 -0500 Received: from pegase.bichat.inserm.fr (mailhost.bichat.inserm.fr [194.57.158.124]) by francois.inserm.fr (8.9.3/dm-199904) with ESMTP id QAA12594 for ; Tue, 6 Nov 2001 16:09:00 +0100 (MET) Received: from bichat.inserm.fr ([194.57.159.81]) by pegase.bichat.inserm.fr (8.9.1b+Sun/8.9.1) with ESMTP id PAA04347 for ; Tue, 6 Nov 2001 15:54:14 GMT Sender: reuter@bichat.inserm.fr Message-ID: <3BE7FD91.D9FE9864@bichat.inserm.fr> Date: Tue, 06 Nov 2001 16:11:13 +0100 From: Reuter Nathalie X-Mailer: Mozilla 4.76 [fr] (X11; U; Linux 2.4.2-2 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: TFE/water boxes AND H3O+ in Charmm Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLer's, I am planning to run MD simulation of a protein in a TFE(tri-fluoroethanol)/water box and I have a few questions on this topic: 1/ Does someone know about TFE parameters in Charmm ? 2/ Does someone know about TFE parameters for other force fields (available for academics) ? 3/ Is it possible to get pre-equilibrated boxes of the mixture like one can get lipids bilayers for example (thanks to people who kindly make them available) ? I have another request if somebody can help : where can I find parameters to model an H3O+ (hydronium) ion in Charmm, (these would of course need to be compatible with the tip3p water as used in Charmm). Thank you very much for your help, Nathalie Reuter -- Nathalie REUTER, PhD U.410 INSERM Faculte de medecine Xavier Bichat 16, rue Henri Huchard BP 416 75870 PARIS Cedex 18 tel : (33) 01.44.85.61.32 fax : (33) 01.42.28.87.65 From chemistry-request@server.ccl.net Tue Nov 6 04:40:08 2001 Received: from mail.takas.lt ([212.59.31.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA69e7B05489 for ; Tue, 6 Nov 2001 04:40:08 -0500 Received: from olegas ([212.59.3.170]) by mail.takas.lt with Microsoft SMTPSVC(5.0.2195.2966); Tue, 6 Nov 2001 11:37:50 +0200 Message-ID: <008101c166af$4f1fab30$aa033bd4@olegas> From: "Olegas Eicher-Lorka" To: Subject: Norm. Coord. Anal. Date: Tue, 6 Nov 2001 11:39:18 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_007E_01C166B7.AB9A29A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-OriginalArrivalTime: 06 Nov 2001 09:37:50.0702 (UTC) FILETIME=[B39BC8E0:01C166A6] This is a multi-part message in MIME format. ------=_NextPart_000_007E_01C166B7.AB9A29A0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, Can anybody ponit me in the direction of some normal coordinate analysis = freeware/shareware. We're using Prometheus, but we're discovering its = limitations. We've tried searching the net for some. but after 4 hours = and filtering we got to under 3 million hits!! Help!!! Olegas ------=_NextPart_000_007E_01C166B7.AB9A29A0 Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
Can anybody ponit me in the direction of some normal = coordinate analysis freeware/shareware. We're using Prometheus, but = we're=20 discovering its limitations. We've tried searching the net for = some. but=20 after 4 hours and filtering we got to under 3 million hits!!=20 Help!!!
 
Olegas
------=_NextPart_000_007E_01C166B7.AB9A29A0-- From chemistry-request@server.ccl.net Tue Nov 6 08:14:04 2001 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6DDwB08682 for ; Tue, 6 Nov 2001 08:13:58 -0500 Received: from desoft1 (desoft01.usc.es [193.144.82.147]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id OAA26027 for ; Tue, 6 Nov 2001 14:17:09 +0100 (MET) Message-ID: <000e01c166c6$0a43ae50$935290c1@usc.es> From: "Armando Navarro" To: Subject: complex exp(x2) integrals Date: Tue, 6 Nov 2001 14:22:08 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C166CE.6B277A50" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C166CE.6B277A50 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Members: Can anybody point me to routines (or simply numerical algorithms) for = solution of complex integrals of the form: int (exp(x2)dx) , with limits between 0 and z, being z a complex number = of the form a+bi.=20 The text in the paper says that this integral can be related to complex = error function, however I was not capable to establish the relationship. Thanks in advance Armando Navarro Facultade de Quimica Departamento de quimica Organica Universidade de Santiago de Compostela. Spain e-mail: qoajnv@usc.es ------=_NextPart_000_000B_01C166CE.6B277A50 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Members:
Can anybody point me to routines (or = simply=20 numerical algorithms) for solution of complex integrals of the=20 form:
 
int (exp(x2)dx) , with limits between 0 = and z,=20 being z a complex number of the form a+bi.
The text in the paper says that this = integral can=20 be related to complex error function, however I was not capable to = establish the=20 relationship.
 
Thanks in advance
Armando Navarro
Facultade de Quimica
Departamento de quimica = Organica
Universidade de Santiago de Compostela. = Spain
e-mail: = qoajnv@usc.es
------=_NextPart_000_000B_01C166CE.6B277A50-- From chemistry-request@server.ccl.net Tue Nov 6 12:57:53 2001 Received: from uk.informa.com ([194.131.213.137]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6HvqB17365 for ; Tue, 6 Nov 2001 12:57:52 -0500 Received: from mort-ex1.uk.informa.com (unverified) by uk.informa.com (Content Technologies SMTPRS 4.2.1) with ESMTP id for ; Tue, 6 Nov 2001 17:53:31 +0000 Received: by mort-ex1.uk.informa.com with Internet Mail Service (5.5.2653.19) id ; Tue, 6 Nov 2001 18:01:24 -0000 Message-ID: <7046152F14C9D511ADCC00508B6A914E477BFF@lonexch_srv.uk.informa.com> From: "Marshall, Chris" To: "'chemistry@ccl.net'" Subject: InfoTechPharma 2002 Announcement Date: Tue, 6 Nov 2001 18:00:44 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/mixed ; boundary="----_=_NextPart_000_01C166EC.F47E56C0" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01C166EC.F47E56C0 Content-Type: text/plain; charset="iso-8859-1" Dear Jan Please find attached a plain text file, summarising InfoTechPharma with relevant web pointers. Kind regards Chris __________________________________ It would be better if you could produce a one page summary of the conference in PLAIN TEXT (no HTML or MS WORD) with pointers to the WEB page: http://www.infotechpharma.com/index.html?src=209 and send this to: chemistry@ccl.net where you would be reaching 3000 people. You do not need to sign up to the list. Jan __________________________________________________ Chris Marshall eMarketing IBC Life Sciences Gilmoora House 57 - 61 Mortimer Street London W1W 8HS Tel: +44 (0)20 7453 5919 Fax: +44 (0)20 7453 5422 chris.marshall@informa.com Visit us on the web! http://www.ibc-lifesci.com/?source=ef Drug Discovery Technology - Europe 15 - 18 April 2002, Stuttgart, Germany http://www.drugdisc.com/?source=ef ********************************************************************** This electronic transmission and any files attached to it are strictly confidential and intended solely for the addressee. If you are not the intended addressee, you must not disclose, copy or take any action in reliance of this transmission. If you have received this transmission in error, please notify us by return and delete the same. Further enquiries/returns can be posted to postmaster@informa.com Thank you. ********************************************************************** ------_=_NextPart_000_01C166EC.F47E56C0 Content-Type: text/plain; name="InfotechPharma 2002.txt" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="InfotechPharma 2002.txt" InfotechPharma 2002: World Informatics Congress for Biopharm R&D http://www.infotechpharma.com/index.html?src=3D209 Wednesday 13 - Thursday 15 February, 2002 InfotechPharma is the annual meeting place for R&D and production = informaticians working in pharma. Discovery, preclinical, clinical and = production professionals from users, vendors and academia gather from = around the world to pick up new ideas and check the ideas they have. = News, reviews, benchmarking and bleeding edge technology combine to = make this event unique. =20 The congress is also home to the fastest growing informatics trade show = around with well over 60 stands due. Targeted breakout sessions for discovery, development and regulatory affairs Option Technologies interactive audience questionnaire on the state of the industry Leading industry speakers and case studies Trade show packed with product launches, seminars, workshops and = mystery keynote speaker Networking events throughout the day, every day Training, networking and poster sessions for junior members of the = informatics community. Sessions include: * Business Strategy * In silico biology * Infrastructure * Regulatory * = Virtual Screening * Architecture * e-Clinical * Alliances * Information = Mgt. * Validation http://www.infotechpharma.com/index.html?src=3D209 ------_=_NextPart_000_01C166EC.F47E56C0-- From chemistry-request@server.ccl.net Tue Nov 6 13:35:18 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6IZIB18521 for ; Tue, 6 Nov 2001 13:35:18 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id NAA18418; Tue, 6 Nov 2001 13:35:17 -0500 (EST) Date: Tue, 6 Nov 2001 13:35:16 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: chris.marshall@informa.com Subject: 02.02.13-14 InfoTechPharma 2002, London, UK Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII InfotechPharma 2002: World Informatics Congress for Biopharm R&D http://www.infotechpharma.com/index.html?src=209 Wednesday 13 - Thursday 15 February, 2002, London, UK InfotechPharma is the annual meeting place for R&D and production informaticians working in pharma. Discovery, preclinical, clinical and production professionals from users, vendors and academia gather from around the world to pick up new ideas and check the ideas they have. News, reviews, benchmarking and bleeding edge technology combine to make this event unique. The congress is also home to the fastest growing informatics trade show around with well over 60 stands due. - Targeted breakout sessions for discovery, development and regulatory affairs _ Option Technologies interactive audience questionnaire on the state of the industry - Leading industry speakers and case studies - Trade show packed with product launches, seminars, workshops and mystery keynote speaker - Networking events throughout the day, every day - Training, networking and poster sessions for junior members of the informatics community. Sessions include: * Business Strategy * In silico biology * Infrastructure * Regulatory * Virtual Screening * Architecture * e-Clinical * Alliances * Information Mgt. * Validation http://www.infotechpharma.com/index.html?src209 Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Tue Nov 6 14:20:45 2001 Received: from mtiwmhc26.worldnet.att.net ([204.127.131.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6JKjB19942 for ; Tue, 6 Nov 2001 14:20:45 -0500 Received: from daveg.fsba.com ([12.72.144.234]) by mtiwmhc26.worldnet.att.net (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20011106192350.BGHS4964.mtiwmhc26.worldnet.att.net@daveg.fsba.com>; Tue, 6 Nov 2001 19:23:50 +0000 Message-Id: <5.1.0.14.0.20011106111328.03002460@pop3.norton.antivirus> X-Sender: davidgallagher/12.17.172.66@pop3.norton.antivirus (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 06 Nov 2001 11:29:08 -0800 To: chemistry@ccl.net From: David Gallagher Subject: Seminars for Medicinal and Synthetic Chemists Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_165835005==_.ALT" --=====================_165835005==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Seminars for Medicinal & Synthetic Chemists San Francisco, CA, Nov 13, 2001, 9:00 - 10.30 a.m. San Jose, CA, Nov 13, 2001, 2:00 - 3.30 p.m. Los Angeles, CA, Nov 14, 2001, 1:00 - 2.30 p.m. San Diego, CA, Nov 15, 2001, 9:00 - 10.30 a.m. Piscataway, NJ, Nov 28, 2001, 2:00 - 3.30 p.m. Philadelphia, PA, Nov 29, 2001, 9:30 - 11.00 a.m. ABSTRACT: Screening virtual libraries of compounds for predicted properties such as solubility, logP, Rule-of-Five, HIA, carcinogenicity, antibacterial activity, etc. will be illustrated with the new BioMedCAChe package for Windows. Use of quantitative structure-property and structure-activity relationships (QSPR & QSAR) to predict any new property will also be reviewed. Examples of homology modeling, structure-based design and pharmacophore-based study will be presented, along with prediction of kinetics, thermodynamics and reaction pathways and application to synthetic chemistry. Chemists use BioMedCAChe to improve their success rate in the laboratory and speed up research by pre-screening candidates and testing their ideas, before investing valuable laboratory time. These free seminars review the expanding scope of computer aided chemistry and are sponsored by Fujitsu. To register contact Kim Hill at 503 746 3602, khill@cachesoftware.com or visit http://www.CACheSoftware.com/news/seminars.shtml David Gallagher --=====================_165835005==_.ALT Content-Type: text/html; charset="us-ascii" Seminars for Medicinal & Synthetic Chemists

   San Francisco, CA, Nov 13, 2001, 9:00 - 10.30 a.m.
   San Jose, CA, Nov 13, 2001, 2:00 - 3.30 p.m.
   Los Angeles, CA, Nov 14, 2001, 1:00 - 2.30 p.m.
   San Diego, CA, Nov 15, 2001, 9:00 - 10.30 a.m.
   Piscataway, NJ, Nov 28, 2001, 2:00 - 3.30 p.m.
   Philadelphia, PA, Nov 29, 2001, 9:30 - 11.00 a.m.

ABSTRACT: Screening virtual libraries of compounds for predicted properties such as solubility, logP, Rule-of-Five, HIA, carcinogenicity, antibacterial activity, etc. will be illustrated with the new BioMedCAChe package for Windows. Use of quantitative structure-property and structure-activity relationships (QSPR & QSAR) to predict any new property will also be reviewed.

Examples of homology modeling, structure-based design and pharmacophore-based study will be presented, along with prediction of kinetics, thermodynamics and reaction pathways and application to synthetic chemistry.

Chemists use BioMedCAChe to improve their success rate in the laboratory and speed up research by pre-screening candidates and testing their ideas, before investing valuable laboratory time. These free seminars review the expanding scope of computer aided chemistry and are sponsored by Fujitsu.

To register contact Kim Hill at 503 746 3602, khill@cachesoftware.com or visit http://www.CACheSoftware.com/news/seminars.shtml

David Gallagher
--=====================_165835005==_.ALT-- From chemistry-request@server.ccl.net Tue Nov 6 14:26:46 2001 Received: from hotmail.com ([216.32.181.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6JQkB20086 for ; Tue, 6 Nov 2001 14:26:46 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 6 Nov 2001 11:29:54 -0800 Received: from 164.68.70.137 by lw2fd.hotmail.msn.com with HTTP; Tue, 06 Nov 2001 19:29:54 GMT X-Originating-IP: [164.68.70.137] From: "Luke Sweet" To: chemistry@ccl.net Subject: g98 Compilation Date: Tue, 06 Nov 2001 11:29:54 -0800 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 06 Nov 2001 19:29:54.0562 (UTC) FILETIME=[697AA620:01C166F9] I am trying to compile the g98 source code (rev A11) on a Pentium 3 running Redhat 7.1. I have installed the Portland Group f77 compiler and I have put the blas-f2c.a and blas-opt.a files in /usr/local/lib. The problem I am having is that the code only compiles to 1402.exe then stops. I have read that people are having problems using g98 with Redhat 7.1. All the suggestions that have been made regarding this problem seem to be corrected the A11 revision of the code. If any one has any suggestions they would be greatly appreciated. Here is the last few lines of the bldg98.log file. bd0402.o(.data+0x1f3a8): multiple definition of `istope_' l402.a(bd0402.o)(.data+0x1f3a8): first defined here bd0402.o(.data+0x1f700): multiple definition of `vsips_' l402.a(bd0402.o)(.data+0x1f700): first defined here bd0402.o(.data+0x20108): multiple definition of `atomic_' l402.a(bd0402.o)(.data+0x20108): first defined here bd0402.o(.data+0x207b8): multiple definition of `twoele_' l402.a(bd0402.o)(.data+0x207b8): first defined here bd0402.o(.data+0x22278): multiple definition of `betas_' l402.a(bd0402.o)(.data+0x22278): first defined here bd0402.o(.data+0x22c80): multiple definition of `onelec_' l402.a(bd0402.o)(.data+0x22c80): first defined here bd0402.o(.data+0x23688): multiple definition of `expont_' l402.a(bd0402.o)(.data+0x23688): first defined here bd0402.o(.data+0x24090): multiple definition of `multip_' l402.a(bd0402.o)(.data+0x24090): first defined here bd0402.o(.data+0x25148): multiple definition of `core_' l402.a(bd0402.o)(.data+0x25148): first defined here bd0402.o(.data+0x254a0): multiple definition of `alpha_' l402.a(bd0402.o)(.data+0x254a0): first defined here bd0402.o(.data+0x257f8): multiple definition of `elemts_' l402.a(bd0402.o)(.data+0x257f8): first defined here bd0402.o(.data+0x258d0): multiple definition of `natorb_' l402.a(bd0402.o)(.data+0x258d0): first defined here make: *** [l402.exe] Error 1 endif Luke Sweet sweetle@lfc.edu Lake Forest College _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Tue Nov 6 19:15:17 2001 Received: from pilsener.srv.ualberta.ca ([129.128.5.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA70FHB25982 for ; Tue, 6 Nov 2001 19:15:17 -0500 Received: from gpu2.srv.ualberta.ca (gpu2.srv.ualberta.ca [129.128.98.45]) by pilsener.srv.ualberta.ca (8.11.6/8.11.1) with ESMTP id fA70IT516239 for ; Tue, 6 Nov 2001 17:18:30 -0700 (MST) Received: from localhost (clovallo@localhost) by gpu2.srv.ualberta.ca (AIX4.3/8.9.3/8.8.5) with ESMTP id RAA49852 for ; Tue, 6 Nov 2001 17:18:30 -0700 Date: Tue, 6 Nov 2001 17:18:29 -0700 (MST) From: C Lovallo X-X-Sender: To: Computational Chemistry List Subject: State-Averaging in GAMESS 09/01 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I just received the Sept. 6, 2001 version of GAMESS and I am running some tests. Does anyone know how to perform state-averaged MCSCF calculations with this new version of GAMESS? To calculate for example the 3F state of the Ti atom, I previously just state-averaged over the lowest seven energy roots with mult=3. However, now GAMESS uses the spatial symmetry in the MCSCF calculation, and of course the seven roots corresponding to the F state have different spatial symmetries. Is it no longer possible to state average roots of different spatial symmetries (without resorting to C1 symmetry), or am I missing something here? Thanks in advance for any help you can give. I'll summarize if interest exists. ************************************************************************** * Christopher Lovallo * * Department of Chemistry * * University of Alberta * * Edmonton, Alberta, Canada * * T6G 2G2 * * E-mail: clovallo@ualberta.ca * ************************************************************************** * If we knew what it was we were doing, it would not be called research, * * would it? * * Albert Einstein * ************************************************************************** From chemistry-request@server.ccl.net Tue Nov 6 17:34:15 2001 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA6MYFB24383 for ; Tue, 6 Nov 2001 17:34:15 -0500 Received: from there (casino.chem.psu.edu [128.118.199.130]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with SMTP id RAA147594 for ; Tue, 6 Nov 2001 17:37:28 -0500 Message-Id: <200111062237.RAA147594@f04n07.cac.psu.edu> Content-Type: text/plain; charset="iso-8859-1" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: chemistry@ccl.net Subject: Equivialnce of connection tables Date: Tue, 6 Nov 2001 17:38:06 -0500 X-Mailer: KMail [version 1.3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Hi, is it possible to decide whether to given connection tables (as supplied in Hyperchem .hin files) are equivilant or not, in an algorithmic manner? Or are there any special formats to which one should convert the file and then analyse the connection table? TIA -- ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 152 Davey Laboratory | web : www.rajarshi.outputto.com Department of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ ------------------------------------------------------------------- A method of solution is perfect if we can forsee from the start, and even prove, that following that method we shall attain our aim. -- Leibnitz From chemistry-request@server.ccl.net Tue Nov 6 21:45:29 2001 Received: from postal.sdsc.edu (IDENT:I8FNh0PmDHkGUUHY0MTrwDFD6W/Coz+B@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA72jTB29051 for ; Tue, 6 Nov 2001 21:45:29 -0500 Received: from koa.sdsc.edu (IDENT:jTmr6OvmAuck1rvkObzSoq9lOxLjlTBM@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/SDSCserver-20) with ESMTP id fA72iPj09133; Tue, 6 Nov 2001 18:44:25 -0800 (PST) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id SAA26539; Tue, 6 Nov 2001 18:44:25 -0800 (PST) Date: Tue, 6 Nov 2001 18:44:25 -0800 From: Wibke Sudholt To: Subject: SUMMARY:Adding hydrogens Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCLers, this is the summary of the answers I got to my question regarding "adding hydrogens". The original question was: "I am searching for free programs that are able to add hydrogens to a given xyz or pdb structure (organic molecule, protein). It would be great if one has some control over this process, e.g. at which atoms how many hydrogens are attached." The following programs were suggested (in alphabetical order): Amber --- http://amber.ch.ic.ac.uk/amber.html ArgusLab --- http://www.planaria-software.com HyperChem Mol2Mol --- http://www.compuchem.com/mol2mol.htm reduce --- http://kinemage.biochem.duke.edu/index.html Swiss-PDB viewer Weblab ViewerLite --- http://www.accelrys.com/products/ WhatIf --- http://www.cmbi.kun.nl/whatif/ , http://cmbi1.cmbi.kun.nl:1100/WIWWWI/ ; Hooft, R.W.W., Sander, C., Vriend, G.: Proteins: Structure, Function, and Genetics 26(1996): 363-376 I had no time to test everything up to now, but as far as I know HyperChem and Mol2Mol are not free and somehow I did not get Swiss-PDB viewer to work in my case. Many thanks for help and interest to (in alphabetical order): Matt Challacombe Denny Chen Mathy Froeyen Tamas E. Gunda Oliver Hucke Ng Pei Ling Sergio Manzetti Mark A. Thompson Arturas Ziemys I hope I did not forget to list anything or anybody! Best regards, Wibke Sudholt University of California, San Diego