From chemistry-request@server.ccl.net Mon Nov 5 02:26:55 2001 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA57QsB27466 for ; Mon, 5 Nov 2001 02:26:55 -0500 Received: from ISOSIRRI (isosirri.csc.fi [193.166.1.218]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id JAA26199 for ; Mon, 5 Nov 2001 09:30:04 +0200 From: "Leif Laaksonen" To: Subject: gOpenMol 2.1 revisited! Date: Mon, 5 Nov 2001 09:29:46 +0200 Message-ID: <001101c165cb$a4d985d0$da01a6c1@ISOSIRRI> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0012_01C165DC.686255D0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3311 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C165DC.686255D0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit I'm very sorry to bug the whole list but this is the after all the most efficient way to reach you all. Stephen P. Molnar reported that one of the main tcl files in the Unix distribution is corrupted! If you have already downloaded gOpenMol, please look at the web page at: http://www.csc.fi/~laaksone/gopenmol/knownbugs.html for instructions how to correct the error. Regards, -leif laaksonen ------=_NextPart_000_0012_01C165DC.686255D0 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;CSC New Technologies TITLE:New Technologies Group Manager NOTE;ENCODING=QUOTED-PRINTABLE:My personal Web page: http://www.csc.fi/~laaksone/=0D=0A=0D=0AMy personal fa= x: +44-870-831-8909=0D=0A=0D=0A=0D=0A TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358500425203 TEL;WORK;FAX:+358 9 457 2302 TEL;HOME;FAX:+44 870 831 8909 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksonen@iki.fi EMAIL;INTERNET:laaksone@csc.fi REV:20010502T202010Z END:VCARD ------=_NextPart_000_0012_01C165DC.686255D0-- From chemistry-request@server.ccl.net Mon Nov 5 07:58:48 2001 Received: from mail.jadeinc.com ([209.57.24.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA5CwlB04118 for ; Mon, 5 Nov 2001 07:58:48 -0500 Received: from smolnar.jadeinc.com [209.57.24.214] by mail.jadeinc.com with ESMTP (SMTPD32-6.06) id AD901D7400F0; Mon, 05 Nov 2001 08:01:04 -0500 Message-Id: <5.1.0.14.2.20011105080146.03451a60@jadeinc.com> X-Sender: smolnar@jadeinc.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 X-Priority: 1 (Highest) Date: Mon, 05 Nov 2001 08:02:05 -0500 To: "Leif Laaksonen" , From: "Stephen P. Molnar, Ph.D." Subject: Re: CCL:gOpenMol 2.1 revisited! In-Reply-To: <001101c165cb$a4d985d0$da01a6c1@ISOSIRRI> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed That solved the problem. At 09:29 AM 11/5/01 +0200, Leif Laaksonen wrote: >I'm very sorry to bug the whole list but this is the after >all the most efficient way to reach you all. > >Stephen P. Molnar reported that one of the main tcl files >in the Unix distribution is corrupted! > >If you have already downloaded gOpenMol, please look at >the web page at: > >http://www.csc.fi/~laaksone/gopenmol/knownbugs.html > >for instructions how to correct the error. > >Regards, > >-leif laaksonen Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Multivariant and stochastic http://web.jadeinc.com/FoundationChem From chemistry-request@server.ccl.net Mon Nov 5 04:52:58 2001 Received: from ra.abo.fi ([130.232.213.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA59qvB32240 for ; Mon, 5 Nov 2001 04:52:57 -0500 Received: from abo.fi (olvi.abo.fi [130.232.210.123]) by ra.abo.fi (8.10.1/8.10.1) with ESMTP id fA59u1r18836; Mon, 5 Nov 2001 11:56:01 +0200 (EET) Sender: jlehtone@ra.abo.fi Message-ID: <3BE66231.58767C0A@abo.fi> Date: Mon, 05 Nov 2001 11:56:01 +0200 From: Jukka Lehtonen Organization: Abo Akademi University X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.8-26mdk i686) X-Accept-Language: fi, en MIME-Version: 1.0 To: chemistry@ccl.net, bioverkko@csc.fi Subject: Announce: Bodil 0.7 (beta-release) modeling environment Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit The Molecular Structures and Biocomputing at the Åbo Akademi University is proud to announce the first public release of Bodil modeling environment version 0.7 beta Bodil is a modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional (OpenGL) molecular graphics closely integrated with sequence viewing and sequence alignment editing. Functionality of Bodil is implemented in dynamically loaded modules. The basic modules provide visualization tools, and protein modeling, small-molecule ligand docking and other modules are currently under development. Bodil version 0.7 beta for Linux(Intel) and SGI Irix is distributed free of charge for non-profit, academic use. Bodil is available for download via the web at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html/ Mail any questions, comments and suggestions to Jukka.Lehtonen@abo.fi -- Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University, Finland From chemistry-request@server.ccl.net Mon Nov 5 11:25:03 2001 Received: from hawk.dcu.ie ([136.206.1.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA5GP3B09189 for ; Mon, 5 Nov 2001 11:25:03 -0500 Received: from dcu.ie (136.206.86.162) by hawk.dcu.ie (6.0.032) id 3BD928A700096DFE for chemistry@ccl.net; Mon, 5 Nov 2001 16:28:29 +0000 Message-ID: <3BE6BE29.17EA038D@dcu.ie> Date: Mon, 05 Nov 2001 16:28:25 +0000 From: Paddy Kane Organization: DCU X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: MD simulation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I am due to demonstrate molecular modelling to several secondary school (high school) students next week. I would like run a molecular dynamics simulation. I am wondering if anyone could supply me with a file that I run with HyperChem. Or is there is a web site where I could download appropriate HyperChem or movie files of MD simulations. I am aware that I can run simulatons while connected to the Internet but the location of the PC to be used in the demonstration will be such that connecting it to the Internet would be very difficult. Therefore, I really would prefer to run the simulations while offline. Best rgds, Paddy. Paddy Kane, Ph.D., MRSC School of Chemical Sciences Dublin City University Dublin 9 Ireland Tel.: +353-1-700-8185 / +353-1-700-8193 Fax: +353-1-700-5503 E-mail: paddy.kane@dcu.ie From chemistry-request@server.ccl.net Mon Nov 5 11:01:57 2001 Received: from garaged.fis.unam.mx ([132.248.33.226]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA5G1uB08330 for ; Mon, 5 Nov 2001 11:01:57 -0500 Received: from yahoo.com (garaged.fis.unam.mx [132.248.33.226]) by garaged.fis.unam.mx (8.11.6/8.11.6) with ESMTP id fA5F65U07893; Mon, 5 Nov 2001 09:06:05 -0600 Sender: max@localhost.localdomain Message-ID: <3BE6AADD.99A2EC1@yahoo.com> Date: Mon, 05 Nov 2001 09:06:05 -0600 From: Max Valdez X-Mailer: Mozilla 4.78 [es] (X11; U; Linux 2.4.13-ac7 i686) X-Accept-Language: en MIME-Version: 1.0 To: Leif Laaksonen CC: chemistry@ccl.net Subject: Re: CCL:gOpenMol 2.1 revisited!(Reason for hang down?) References: <001101c165cb$a4d985d0$da01a6c1@ISOSIRRI> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Is that the reason to gopenmol take ALL the memory on a linux box and hanging it down ? Max From chemistry-request@server.ccl.net Mon Nov 5 17:36:49 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fA5MamB25162 for ; Mon, 5 Nov 2001 17:36:48 -0500 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id RAA25122; Mon, 5 Nov 2001 17:38:17 -0500 (EST) Message-ID: <3BE71472.9322E9C2@mindless.com> Date: Mon, 05 Nov 2001 17:36:34 -0500 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: a3arzi CC: sanner@scripps.edu, CCL Subject: Re: CCL:ADT error .. need help References: <43247335.20011102152410@vaidila.vdu.lt> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ADT runs a csh and not on bash which does linux. Here is the initPython in bash: # !/bin/bash -f # export ROOT="$(pwd)" export PATH="$ROOT/i86Linux2/bin:$PATH" export PYTHONHOME="$ROOT/share:$ROOT/i86Linux2" export TCL_LIBRARY="$ROOT/tcl8.3" export TK_LIBRARY="$ROOT/tk8.3" export TCLLIBPATH="$ROOT/i86Linux2/extralibs" shlibdirs="$ROOT/i86Linux2/lib:$ROOT/i86Linux2/extralibs" if test -z "$LD_LIBRARY_PATH" then export LD_LIBRARY_PATH="$shlibdirs" else export LD_LIBRARY_PATH="$shlibdirs:$LD_LIBRARY_PATH" fi Save it in ./initPythonbash where the initPython is , source it and then try to run python2.0. If it works put those lines in your .cshrc, Let me know if it worked for you. David Smith a3arzi wrote: > > Hello, > > I installed ADT undr linux (Suse 7.0, kernel 2.4.x). My python runs > (/usr/bin/env python). I have corrected 'adt' executable first line: > #!/usr/bin/env python1.5.2 -> #!/usr/bin/env python in oder it could > run at all. My ADT package was decompressed as follos : > /home/'my dir'/share/lib/python1.5/site-packages/AutoDockTools > /home/'my dir'/i86linux2/.... > > Made alias to 'adt' as well. But when I run in bash prompt 'adt' I get the > following error: > > > '...my path to adt...' line 40, in ? > import AutoDockTools > ImportError: No modules named AutoDockTools > hit any .... > > What is wrong ? > > I got another directory i86linux2. What is the relation > with 'adt' ? > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Nov 5 20:20:52 2001 Received: from mail.utexas.edu ([128.83.126.138]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fA61KqB29870 for ; Mon, 5 Nov 2001 20:20:52 -0500 Received: (qmail 17639 invoked by uid 0); 6 Nov 2001 01:24:03 -0000 Received: from dhcp-164-217.phr.utexas.edu (HELO naphthyl.phr.utexas.edu) (128.83.164.217) by umbs-smtp-3 with SMTP; 6 Nov 2001 01:24:03 -0000 Message-ID: <3BE73C7A.90DA318B@naphthyl.phr.utexas.edu> Date: Mon, 05 Nov 2001 19:27:22 -0600 From: "Robert S. Pearlman" X-Mailer: Mozilla 4.75 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, qsar_society@msi.com Subject: Final Reminder: April 2002 ACS "Lead Follow-up" Symposium] Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello again -- The November 12th deadline for submitting papers to all COMP symposia is just one week away. This is a last-chance reminder to submit abstracts for the Symposium on "Near-Neighbor Searching for Lead Follow-up" to be held at the ACS Meeting in Orlando FL this coming April. Best wishes to all ... On October 10 2001, "Robert S. Pearlman" wrote: > > Hello -- > > The November 12th deadline for submitting papers to the April 2002 ACS > Symposium on "Near-Neighbor Searching for Lead Follow-up: Algorithms > and Descriptors" is rapidly approaching. I have already accepted some > excellent abstracts and am eager to accept more. However, we only have > room in the Symposium for a limited number of presentations. Thus, I > suspect that I will be forced to make some difficult choices about which > abstracts to include in the Symposium and which to recommend for general > podium presentation. At some point, the date an abstract is submitted > will become a factor in this decision-making process so I encourage you > to submit your abstract as soon as possible. > > A copy of the original call-for-papers is appended below but please note > the > NEW 2-STEP INSTRUCTIONS FOR SUBMITTING AN ABSTRACT: > 1. Please submit your abstract through the OASYS facility. Point your > browser to: http://oasys.acs.org/acs/223nm/comp/papers/index.cgi and > click the button for the "Near-neighbor searching ..." Symposium. > Please be sure to follow the formatting instructions provided by OASYS. > 2. Please e-mail a copy of your abstract to me at > pearlman@list.phr.utexas.edu. > > CALL-FOR-PAPERS: > > > April 2002 ACS Symposium on "Near-Neighbor Searching for Lead > Follow-up: > > Algorithms and Descriptors" > > > > As its name suggests this symposium will address: (1) novel > algorithms or methods > > related to near-neighbor searching in the context of lead follow-up > and (2) molecular > > descriptors useful for near-neighbor searching in the context of lead > follow-up. > > In addition (and if space on the program permits), the symposium will > also address: > > (3) "success stories" in using near-neighbor searching in the context > of lead follow-up. > > > > The deadline for submitting abstracts is November 12th. Please e-mail > abstracts to: > > I'm looking forward to seeing you in Orlando in April. > > Best wishes, > > -- Bob > > Robert S. Pearlman, Ph.D > Coulter R. Sublett Regents Chair in Pharmacy and > Director, Laboratory for the Development of > Computer-Assisted Drug Discovery Software > College of Pharmacy > University of Texas > Austin, Texas 78712 > 512-471-3383 (voice) > 512-471-7474 (FAX) > pearlman@naphthyl.phr.utexas.edu From chemistry-request@server.ccl.net Mon Nov 5 16:41:59 2001 Received: from web13403.mail.yahoo.com ([216.136.175.61]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fA5LfxB23258 for ; Mon, 5 Nov 2001 16:41:59 -0500 Message-ID: <20011105214511.25994.qmail@web13403.mail.yahoo.com> Received: from [169.232.140.206] by web13403.mail.yahoo.com via HTTP; Mon, 05 Nov 2001 13:45:11 PST Date: Mon, 5 Nov 2001 13:45:11 -0800 (PST) From: eric hu Subject: flat potential surface To: CHEMISTRY@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear ALL, If the potential surface happens to be flat at the transition state region, what is the best way to find the 1st transition state. I tried to use conventional optimization method in G98 and it always produced an imaginary frequency which is not along the reaction coordinate. Eric __________________________________________________ Do You Yahoo!? Find a job, post your resume. http://careers.yahoo.com