From chemistry-request@server.ccl.net Mon Jun 24 18:28:07 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5OMS6Q21072 for ; Mon, 24 Jun 2002 18:28:06 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g5OMb8n19038 for chemistry@ccl.net; Mon, 24 Jun 2002 15:37:08 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g5OMb7Y19029 for ; Mon, 24 Jun 2002 15:37:07 -0700 To: chemistry@ccl.net Subject: Accelrys Customer Training on InsightII in Munich MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Mon, 24 Jun 2002 15:27:55 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 06/24/2002 03:27:57 PM, Serialize complete at 06/24/2002 03:27:57 PM Content-Type: text/plain; charset="us-ascii" Accelrys Inc. will be holding a pair of 2-day workshops at our office in Munich, Germany, in July 2002. On July 2-3, the workshop "Introduction to Life Science Modeling with InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling. On July 4-5, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step. Both manual and automatic methodologies will be discussed. Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII. Fees for each 2-day course are Euro 1108 commercial, Euro 831 government, and Euro 609 academic. Registration is on-line at URL http://www.accelrys.com/training/macro/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/macro/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 1-858-799-5555 Judith Madeley +44 1223 228 609 -- Jeffrey L. Nauss, Ph.D. Manager US Training, Global Bioinformatics and Macromolecular Modeling Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Tue Jun 25 09:56:47 2002 Received: from mh1-cam.cam.accelrys.com ([192.190.183.253]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5PDukW11331 for ; Tue, 25 Jun 2002 09:56:46 -0400 Received: from camdmail01.cam.accelrys.com ([172.27.160.90]) by mh1-cam.cam.accelrys.com with esmtp (Exim 3.12 #1 (Debian)) id 17MqoF-0007KR-00 for ; Tue, 25 Jun 2002 14:56:43 +0100 To: chemistry@ccl.net Subject: Accelrys Cerius2 Training in North Carolina MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: From: tluu@accelrys.com Date: Tue, 25 Jun 2002 14:56:41 +0100 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 06/25/2002 01:56:41 PM, Serialize complete at 06/25/2002 01:56:41 PM Content-Type: multipart/alternative; boundary="=_alternative 004C991D80256BE3_=" This is a multipart message in MIME format. --=_alternative 004C991D80256BE3_= Content-Type: text/plain; charset="us-ascii" Accelrys Inc. will be holding two workshops involving the Cerius2 user interface at the North Carolina Supercomputing Center, Research Triangle Park, North Carolina in September 2002. The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on September 17-18. This course provides an overview of molecular modelling techniques for life sciences applications using Cerius2. The workshop will focus on basic skills for use of the interface and will explore various modules in the areas of rational-drug design, structure-based drug design, and combinatorial chemistry. Prior modelling experience is not assumed making this course a great place to learn molecular modelling with Cerius2. On September 19-20, the " Small Molecule and Drug Design with Cerius2" workshop will be offered. This workshop is aimed at our customers who are involved in drug design or the development of other bioactive compounds and who would like to make more effective use of modelling in their research. The course will focus on QSAR techniques and methodologies as well as structure-based ligand design. Attendees should possess knowledge of basic UNIX commands and have a basic understanding of QSAR theory. Familiarity with the Cerius2 environment is required for attendance to this workshop. Both suggested prerequisites can be met by attending the introductory workshop. Fees for each 2-day course are $1200 commercial, $900 government, and $660 academic. Registration is on-line at URL http://www.accelrys.com/training/rdd/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/rdd/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Tien Luu +44 1223 228 608 Judith Madeley +44 1223 228 609 --=_alternative 004C991D80256BE3_= Content-Type: text/html; charset="us-ascii"
Accelrys Inc. will be holding two workshops involving the Cerius2 user
interface at the North Carolina Supercomputing Center, Research
Triangle Park, North Carolina in September 2002.

The "Introduction to Cerius2 for Life Sciences Workshop" will be offered on
September 17-18.  This course provides an overview of molecular modelling
techniques for life sciences applications using Cerius2.  The workshop will
focus on basic skills for use of the interface and will explore various
modules in the areas of rational-drug design, structure-based drug design,
and combinatorial chemistry.  Prior modelling experience is not assumed
making this course a great place to learn molecular modelling with Cerius2.

On September 19-20, the " Small Molecule and Drug Design with Cerius2" workshop
will be offered.  This workshop is aimed at our customers who are involved in
drug design or the development of other bioactive compounds and who would
like to make more effective use of modelling in their research.  The course will
focus on QSAR techniques and methodologies as well as structure-based
ligand design.  Attendees should possess knowledge of basic UNIX
commands and have a basic understanding of QSAR theory.  Familiarity
with the Cerius2 environment is required for attendance to this workshop.  
Both suggested prerequisites can be met by attending the introductory workshop.

Fees for each 2-day course are $1200 commercial, $900 government,
and $660 academic.

Registration is on-line at URL
http://www.accelrys.com/training/rdd/registration.php.  Further detailed
information about this and other Accelrys training workshops can be found
at the Accelrys website
(http://www.accelrys.com/training/rdd/schedule.html).

Please do not hesitate to contact us should you have any questions.

Thank you very much.

Tien Luu
+44 1223 228 608
Judith Madeley
+44 1223 228 609





 --=_alternative 004C991D80256BE3_=-- From chemistry-request@server.ccl.net Tue Jun 25 04:30:05 2002 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5P8U5W10123 for ; Tue, 25 Jun 2002 04:30:05 -0400 Received: by hpserv.imim.es with Internet Mail Service (5.5.2655.55) id ; Tue, 25 Jun 2002 10:32:28 +0200 Received: from imim.es (i21.imim.es [193.147.240.127]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2655.55) id NF4Y8VZ5; Tue, 25 Jun 2002 10:32:24 +0200 From: =?iso-8859-1?Q?=22Teran_Casta=F1on=2C_Hugo_Gutierrez_de=22?= To: ccl Message-ID: <3D1829DD.BBD397D6@imim.es> Date: Tue, 25 Jun 2002 10:29:17 +0200 X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.4.2-2 i686) X-Accept-Language: en MIME-Version: 1.0 Subject: Autodock bad energies and positions Content-Type: multipart/alternative; boundary="------------EC9725805BCC977A9081976A" --------------EC9725805BCC977A9081976A Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit For the Autodock users community: I have obtained bad results from a docking experiment with Autodock default parameters (CONH atom types, 12-6 lj for N), in order of energies (-30000 kcal/mol, unreallistically good) and position (legand clearly shows bumps with the protein). on the mayority of solutions found. Does anyone have expirience on such Autodock results? If I change parameters (12-10 hb for N, and creating a new atom type 12-6 lj for nitrogen that does not accept H-bonds, and considering only polar H on my ligand) solutions are more reallistic, but don't agree with experimental data. Anyone have expirience on changing Autodock default parameters or creating new atom types? Thanks in advance, Hugo -- Hugo G. de Teran Castañon Drug Design laboratory Research Group on Biomedical Informatics (GRIB) - IMIM/UPF C/ Dr. Aiguader, 80 Tel: +34 93 221 1009 E-08003 Barcelona (Spain) Fax: +34 93 221 3237 e-mail: hteran@imim.es http://www.imim.es/grib/ --------------EC9725805BCC977A9081976A Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit For the Autodock users community:
I have obtained bad results from a docking experiment with Autodock default parameters (CONH atom types, 12-6 lj for N), in order of energies (-30000 kcal/mol, unreallistically good) and position (legand clearly shows bumps with the protein). on the mayority of solutions found.
Does anyone have expirience on such Autodock results?
If I change parameters (12-10 hb for N, and creating a new atom type 12-6 lj for nitrogen that does not accept H-bonds, and considering only polar H on my ligand) solutions are more reallistic, but don't agree with experimental data.
Anyone have expirience on changing Autodock default parameters or creating new atom types?
Thanks in advance,
Hugo 
-- 
Hugo G. de Teran Castañon
Drug Design laboratory
Research Group on Biomedical Informatics (GRIB) - IMIM/UPF

C/ Dr. Aiguader, 80                     Tel: +34 93 221 1009
E-08003 Barcelona (Spain)               Fax: +34 93 221 3237
e-mail: hteran@imim.es         http://www.imim.es/grib/
  --------------EC9725805BCC977A9081976A-- From chemistry-request@server.ccl.net Tue Jun 25 07:20:49 2002 Received: from relay.unizar.es ([155.210.11.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5PBKlW28218 for ; Tue, 25 Jun 2002 07:20:47 -0400 Received: from celes.unizar.es (celes.unizar.es [155.210.11.15]) by relay.unizar.es (8.12.3/8.12.3) with ESMTP id g5PBJRMk016539; Tue, 25 Jun 2002 13:19:27 +0200 Received: from there (santiago@[155.210.93.83]) by celes.unizar.es (8.11.1/8.11.1) with SMTP id g5PBJos00801; Tue, 25 Jun 2002 13:19:50 +0200 (MET DST) Message-Id: <200206251119.g5PBJos00801@celes.unizar.es> Content-Type: text/plain; charset="iso-8859-1" From: Santiago Cuesta <405137@docto.unizar.es> Reply-To: 405137@docto.unizar.es Organization: Ciencias To: ako@cse.nd.edu Subject: charmm problems Date: Tue, 25 Jun 2002 13:18:37 +0200 X-Mailer: KMail [version 1.3.2] Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Virus-Scanned: TAMIZ + Sophos en unizar.es Hi Alice ! 1) One way to balance charge is adding Na+ to your system. In your case ...9 Na+ ... ... how to add in CHARMM is easy, but WHERE to add it's a problem ... One possibility is to place the ions close to the charged residues, making sure that there is no overlapping with the protein. I prefer to make a little script that generates ions at random positions , then I use some criteria to accept them or not (like electrostatics, overlap, etc ...). After that, I think it's a good strategy to complete the neutralization performing a short "equilibration". (fix the residues, and allow the ions and solvent to accomodate). 2) y 3) Maybe these references will help you to understand minimization and dynamics analysis: To begin understanding CHARMM and molecular simulations search in the net these : "Übungen zu NMR-Spektroskopie und Biomolekularer Simulation" by Stefan Boresch (1999) (It's in english) " Introduction to Macromolecular Simulation" by Peter J. Steinbach Good tutorials are: http://www.ch.embnet.org/MD_tutorial/ http://www.sinica.edu.tw/~scimath/msi/insight2K/charmm_principles/Ch04_mol_dyn.FM5.html#678970 I hope last one will answer all your problems. Finally you can find some charmm examples in: http://www.psc.edu/general/software/packages/charmm/example_input/ Bye !! Yours Sincerely Santiago Cuesta ------------------------------------ Santiago Cuesta López Dep. Física de la Materia Condensada. Grupo de Simulación de Sistemas Complejos Universidad de Zaragoza. (Spain) e-mail: 405137@docto.unizar.es From chemistry-request@server.ccl.net Mon Jun 24 18:28:06 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5OMS5Q21071 for ; Mon, 24 Jun 2002 18:28:05 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g5OMb6e19007 for chemistry@ccl.net; Mon, 24 Jun 2002 15:37:06 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g5OMb5Y18998 for ; Mon, 24 Jun 2002 15:37:06 -0700 To: chemistry@ccl.net Subject: Accelrys Bioinformatics Workshops in San Diego MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Mon, 24 Jun 2002 15:27:53 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 06/24/2002 03:27:55 PM, Serialize complete at 06/24/2002 03:27:55 PM Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g5OMS6Q21073 Accelrys Inc. will be holding three bioinformatics workshops at our office in San Diego, CA, July 16-19. On July 16-17, the workshop "Wisconsin Package and SeqLab" will be offered. The GCG Wisconsin Package® is the most widely used bioinformatics suite in the world. Containing over 130 programs, it covers almost every aspect of sequence analysis. This workshop describes the use of the Wisconsin Package through the X-Windows interface SeqLab®. Many of the basic functions are described in detail with enough theoretical description to obtain an understanding of many of the programs. No prior experience with the Wisconsin Package is required but some knowledge of bioinformatics techniques will be helpful. On July 18, the one-day "SeqWeb Workshop" will be offered. This workshop is relevant to customers who already know about the Wisconsin Package but who would like to use a web-based interface. SeqWeb provides intranet access to some of the more popular applications in the Wisconsin Package > from a web browser. A prerequisite for this course is experience with the Wisconsin Package or completion of the "Wisconsin Package and SeqLab Workshop". Finally, on July 19, the one-day "Desktop Visualization and Communication with ViewerPro Workshop" will be conducted. This workshop is designed for chemists, biochemists, biologists, or anyone else who wants high-quality molecular modeling, visualization, and analysis on their desktop. This one-day workshop focuses on the use of Viewer Pro with Microsoft desktop products for communication and integration. It is an excellent complement to the Wisconsin Package training for the visualization of protein structures. Fees per individual for the 2-day "Wisconsin Package and SeqLab Workshop" are $1200 commercial, $900 government/nonprofit, and $660 academic. Fees for either the "SeqWeb" or the "Desktop Visualization and Communication with ViewerPro" workshops are $600 commercial, $450 government/nonprofit, or $330 academic each. Registration is on-line at URL http://www.accelrys.com/training/bioinf/schedule.html. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/index.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Pei-Li Li 858-799-5471 -- Jeffrey L. Nauss, Ph.D. Manager US Training, Global Bioinformatics and Macromolecular Modeling Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Mon Jun 24 23:27:33 2002 Received: from mail.useoz.com ([203.220.32.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5P3RWQ05343 for ; Mon, 24 Jun 2002 23:27:32 -0400 Received: from [203.194.10.109] (helo=user) by mail.useoz.com with smtp (Exim 3.36 #1) id 17Mgvt-0006PH-00 for chemistry@ccl.net; Tue, 25 Jun 2002 13:23:58 +1000 Message-ID: <005001c21bf8$43725180$0100a8c0@user> Reply-To: "DrHuang" From: "DrHuang" To: Subject: Fw: RunTime error 13 in chemistry software Polar Date: Tue, 25 Jun 2002 13:27:39 +1000 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 8bit 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 ----- Original Message ----- From: "DrHuang" To: Sent: Thursday, June 20, 2002 5:05 PM Subject: re: RunTime error 13 in Polar > > ----- Original Message ----- > From: "DrHuang" > Sent: Thursday, June 20, 2002 4:06 PM > Subject: Re: Polar > > > > Please read its FAQ on its document: > > > > Q: When I click the Simulate menu, I got error: ¡°No data¡±, or "Run-time > > error 13¡±, with the message: "Type mismatch". > > > > A: I guess you are running it under non-English version of Windows. Please > > change language setting to English in the Regional Setting of the Control > > Panel, and restart Polar. Or try it under English version of Windows. Some > > non-English versions of Windows have problem to run English version > program. > > > > > > > > ----- Original Message ----- > > To: "DrHuang" > > Sent: Wednesday, June 19, 2002 9:49 PM > > Subject: Re: Polar > > > > > > > Dr. Huang, > > > I tried to install in my office PC. However, > > > on running polar.exe it gave an error saying > > > RunTime error '13'. > > > I made a copy of the downloaded file (~1.6 MB) > > > to my office from my home. > > > The home pc also started giving me the same error. > > > Downloading fresh one was also resulted in same > > > error. > > > Suggest a solution > > > thank you > > > venkatesan From chemistry-request@server.ccl.net Tue Jun 25 16:13:35 2002 Received: from mail-mta2.service.ohio-state.edu ([128.146.216.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5PKDZW04815 for ; Tue, 25 Jun 2002 16:13:35 -0400 Received: from osu.edu (laba-pc22.pharmacy.ohio-state.edu [128.146.80.238]) by mail-mta2.service.ohio-state.edu (iPlanet Messaging Server 5.1 HotFix 0.6 (built Apr 26 2002)) with ESMTP id <0GYA005M22UIR8@mail-mta2.service.ohio-state.edu> for chemistry@ccl.net; Tue, 25 Jun 2002 16:13:31 -0400 (EDT) Date: Tue, 25 Jun 2002 16:13:30 -0400 From: Praveen Bahadduri Subject: Protein Modelling Sender: praveen@osu.edu To: chemistry@ccl.net Message-id: <3D18CEEA.598CB1EC@osu.edu> Organization: The Ohio-State University MIME-version: 1.0 X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Hello! CCL! I had question about the protein homology modelling. Does anyone know how we place/model a METAL atom onto a metalloprotein homology model? If somebody has refernces related to this quesion, please let me know. Praveen The Ohio-State University Columbus, OH From chemistry-request@server.ccl.net Tue Jun 25 19:08:56 2002 Received: from trivial.uchicago.edu (IDENT:root@[128.135.160.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5PN8uW12933 for ; Tue, 25 Jun 2002 19:08:56 -0400 Received: from localhost (cmtaylor@localhost) by trivial.uchicago.edu (8.9.3/8.9.3) with ESMTP id SAA18083 for ; Tue, 25 Jun 2002 18:08:54 -0500 Date: Tue, 25 Jun 2002 18:08:54 -0500 (CDT) From: Caroline Taylor To: CCL list Subject: Basis Functions for Ca Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all. I am trying to find a basis set which has g functions for Ca (or even just the g functions part). The sets contained in the EMSL library only go through d orbitals for Ca. Can somebody point me in the right direction? Thanks! -Caroline -- --------------------------------------------- Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 --------------------------------------------- From chemistry-request@server.ccl.net Tue Jun 25 18:01:58 2002 Received: from mercury.chem.northwestern.edu (root@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5PM1wW08129 for ; Tue, 25 Jun 2002 18:01:58 -0400 Received: from HaitaoJI (che116237.chem.northwestern.edu [129.105.116.237]) by mercury.chem.northwestern.edu (8.11.6+Sun/8.11.6) with SMTP id g5PM1x006424 for ; Tue, 25 Jun 2002 17:01:59 -0500 (CDT) Message-ID: <000801c0fdc2$739f33f0$9865fea9@HaitaoJI> From: "Haitao Ji" To: Subject: the gawk Date: Mon, 25 Jun 2001 16:01:56 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C0FD90.28A2F4E0" 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_0005_01C0FD90.28A2F4E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, everyone When I run the AutoDock3.0. I meet a problem as listed in the following: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ % mol2topdbq tes1.mol2 gawk - Command not found % pdbsplitchains test.pdb /disk2/jht/program/autodock/share/pdbsplitchains[2]: gawk: not found ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ What should I do?=20 Thank you Haitao Ji, Ph.D. Department of Chemistry Northwestern University 2145 Sheridan Road Evanston, IL 60208 Email: jihaitao@chem.nwu.edu ------=_NextPart_000_0005_01C0FD90.28A2F4E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, everyone
 
When I run the AutoDock3.0. I=20 meet a problem as listed in the following:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
% mol2topdbq tes1.mol2
gawk - = Command not=20 found
% pdbsplitchains=20 test.pdb
/disk2/jht/program/autodock/share/pdbsplitchains[2]: = gawk:  not=20 found
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
What should I do?
 
Thank you
 
Haitao Ji, Ph.D.
Department of Chemistry
Northwestern University
2145 Sheridan Road
Evanston, IL 60208
Email: jihaitao@chem.nwu.edu
------=_NextPart_000_0005_01C0FD90.28A2F4E0-- From chemistry-request@server.ccl.net Tue Jun 25 17:08:50 2002 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5PL8oW06946 for ; Tue, 25 Jun 2002 17:08:50 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g5PL8op25613 for ; Tue, 25 Jun 2002 14:08:50 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 21492; Tue, 25 Jun 2002 14:03:54 -0700 (PDT) Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay2.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g5PL8eu10075 for ; Tue, 25 Jun 2002 14:08:40 -0700 (PDT) Received: from aaron (aaron [137.131.108.91]) by goliath.scripps.edu (SGI-8.9.3/TSRI-3.0.1) with SMTP id OAA45445; Tue, 25 Jun 2002 14:08:40 -0700 (PDT) Message-Id: <200206252108.OAA45445@goliath.scripps.edu> Date: Tue, 25 Jun 2002 14:08:40 -0700 (PDT) From: Michel Sanner Reply-To: Michel Sanner Subject: Python for scientific computing To: CHEMISTRY@ccl.net Cc: sanner@scripps.edu MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: OMFkt4TIKLuw6HIF6NBagg== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.4.2 SunOS 5.8 sun4u sparc Hello, This is an announcement for a workshop on Python for Scientific Computing. This first edition of the workshop will have a strong emphasis on molecular sciences. Please visit the web site http://www.scipy.org/site_content/scipy02 for registration and more information about the workshop. Attendance has been limited to 50 participants. Best regards, ---------------------------------------- Python for Scientific Computing Workshop ---------------------------------------- CalTech, Pasadena, CA Septemer 5-6, 2002 http://www.scipy.org/site_content/scipy02 This workshop provides a unique opportunity to learn and affect what is happening in the realm of scientific computing with Python. Attendees will have the opportunity to review the available tools and how they apply to specific problems. By providing a forum for developers to share their Python expertise with the wider industrial, academic, and research communities, this workshop will foster collaboration and facilitate the sharing of software components, techniques and a vision for high level language use in scientific computing. The two-day workshop will be a mix of invited talks and training sessions in the morning. The afternoons will be breakout sessions with the intent of getting standardization of tools and interfaces. The cost of the workshop is $50.00 and includes 2 breakfasts and 2 lunches on Sept. 5th and 6th, one dinner on Sept. 5th, and snacks during breaks. There is a limit of 50 attendees. Should we exceed the limit of 50 registrants, the 50 persons selected to attend will be invited individually by the organizers. Discussion about the conference may be directed to the SciPy-user mailing list: mailto:scipy-user@scipy.org http://www.scipy.org/MailList ------------- Co-Hosted By: ------------- The National Biomedical Computation Resource (NBCR, SDSC, San Diego, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu The mission of the National Biomedical Computation Resource at the San Diego Supercomputer Center is to conduct, catalyze, and enable biomedical research by harnessing advanced computational technology. The Center for Advanced Computing Research (CACR, CalTech, Pasadena, CA) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ http://nbcr.sdsc.edu CACR is dedicated to the pursuit of excellence in the field of high-performance computing, communication, and data engineering. Major activities include carrying out large-scale scientific and engineering applications on parallel supercomputers and coordinating collaborative research projects on high-speed network technologies, distributed computing and database methodologies, and related topics. Our goal is to help further the state of the art in scientific computing. Enthought, Inc. (Austin, TX) ^^^^^^^^^^^^^^^ http://enthought.com Enthought, Inc. provides business and scientific computing solutions through software development, consulting and training. Enthought also fosters the development of SciPy, an open source library of scientific tools for Python. _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.net http://www.scipy.net/mailman/listinfo/scipy-dev ----------------------------------------------------------------------- Michel F. Sanner Ph.D. The Scripps Research Institute Assistant Professor Department of Molecular Biology 10550 North Torrey Pines Road Tel. (858) 784-2341 La Jolla, CA 92037 Fax. (858) 784-2860 sanner@scripps.edu http://www.scripps.edu/sanner ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jun 25 14:39:49 2002 Received: from hotmail.com ([64.4.15.164]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5PIdmW28257 for ; Tue, 25 Jun 2002 14:39:49 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 25 Jun 2002 11:39:44 -0700 Received: from 128.235.242.51 by lw10fd.law10.hotmail.msn.com with HTTP; Tue, 25 Jun 2002 18:39:43 GMT X-Originating-IP: [128.235.242.51] From: "Deepangi Pandit" To: chemistry@ccl.net Subject: Analyze menu of ADT (Autodock Tools) of Autodock 3.0 Date: Tue, 25 Jun 2002 14:39:43 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 25 Jun 2002 18:39:44.0386 (UTC) FILETIME=[ACB27E20:01C21C77] Hello: I am curious to know about Analyze menu of ADT (Autodock Tools) of Autodock 3.0 as in my case it is not working at all. I cannot see docked conformation using Analyze menu. AutoDock users, please let me know about your dockings, are you able to use Analyze menu. Secondly in my case autogrid3 command works but autodock3 command does not work and I use autodock command so I feel in .dlg file it is mentions AutoDock 3.0 Beta version and gives me output whereas I want to get .dlg using version 3.0.5. Please let me know what menu work in your case or you just use commands from command line.Whether above mentioned problems are installation based or something else. Thank you Deepangi _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx