From owner-chemistry@ccl.net Wed Aug 1 10:38:00 2007 From: "Martin Graf graf[#]mpi-muelheim.mpg.de" To: CCL Subject: CCL: software for equipotential lines ? Message-Id: <-34838-070801084226-18851-kqkLE4hJP9LyI48kxPU80w-.-server.ccl.net> X-Original-From: Martin Graf Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Aug 2007 14:12:27 +0200 MIME-Version: 1.0 Sent to CCL by: Martin Graf [graf^mpi-muelheim.mpg.de] Michael Shokhen shokhen]=[mail.biu.ac.il wrote: > > I would appreciate if somebody can address me to a graphical > software (for Windows) for equipotential lines building > ( presentation of 2D potential surface, E(x,y)). > The feature of my data points, E(x,y), is that X and Y coordinates > are chaotically distributed over the (X,Y) plane, so E(x,y) cannot be organized in a regular rectangular grid (table with rows and columns enumerated according to fixed X and Y values, so Excel graphical tools > are usless here. Have you considered using gnuplot? It is not the most pretty interface ever, but it does a good job if you have weird data formats. Regards, Martin From owner-chemistry@ccl.net Wed Aug 1 11:45:00 2007 From: "Andrew Colasanti acolasanti*gmail.com" To: CCL Subject: CCL: Workflow management/web services software Message-Id: <-34839-070801114245-2088-TKJUA1UeCFFtb7agft0p7g]~[server.ccl.net> X-Original-From: "Andrew Colasanti" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 1 Aug 2007 11:42:32 -0400 MIME-Version: 1.0 Sent to CCL by: "Andrew Colasanti" [acolasanti.+/-.gmail.com] I am looking into workflow management software and wanted to know about experiences and suggestions. The three that I am thinking about are 1) Taverna (taverna.sourceforge.net) 2) Knime (www.knime.org) 3) Kepler (kepler-project.org) I also know about Pipeline Pilot from SciTegic/Accelrys but the cost is prohibitive. I am also interested in the use of CDK and Openbabel within the software. The projects will be chem-/bioinformatics based. Thanks in advance Andrew From owner-chemistry@ccl.net Wed Aug 1 14:39:01 2007 From: "Mesa Analytics & Computing, LLC mesaac.:.comcast.net" To: CCL Subject: CCL: Workflow management/web services software Message-Id: <-34840-070801134755-19021-Lxe+Zo4vUtScjk8dhjAMZg=-=server.ccl.net> X-Original-From: "Mesa Analytics & Computing, LLC" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 1 Aug 2007 11:16:16 -0600 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: "Mesa Analytics & Computing, LLC" [mesaac::comcast.net] Another is VisiQuest by AccuSoft. http://www.accusoft.com/products/ visiquest/overview.asp It has a full development environment and we have built cheminformatics/molecular modeling workflows with it. It is very powerful, along the lines of AVS Express, but less expensive than Pipeline Pilot. You can incorporate and/or otherwise launch other software from the workflow(s). Cheers, Norah ---------------------------- Norah MacCuish, Ph.D. CSO Mesa Analytics & Computing, LLC www.mesaac.com On Aug 1, 2007, at 9:42 AM, Andrew Colasanti acolasanti*gmail.com wrote: > > Sent to CCL by: "Andrew Colasanti" [acolasanti.],[.gmail.com] > I am looking into workflow management software and wanted to know > about experiences and suggestions. The three that I am thinking about > are > > 1) Taverna (taverna.sourceforge.net) > 2) Knime (www.knime.org) > 3) Kepler (kepler-project.org) > > I also know about Pipeline Pilot from SciTegic/Accelrys but the cost > is prohibitive. > > I am also interested in the use of CDK and Openbabel within the > software. The projects will be chem-/bioinformatics based. > > Thanks in advance > > Andrew > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Wed Aug 1 15:14:00 2007 From: "Rosalie Peck rosaliepeck : gmail.com" To: CCL Subject: CCL: input files for TINKER Message-Id: <-34841-070731181541-7538-6Rw5uW0NhbZK4J0M7JDS4g::server.ccl.net> X-Original-From: "Rosalie Peck" Content-Type: multipart/alternative; boundary="----=_Part_49245_5380917.1185916252708" Date: Tue, 31 Jul 2007 17:10:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Rosalie Peck" [rosaliepeck|gmail.com] ------=_Part_49245_5380917.1185916252708 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Is it possible to create a z-matrix for TINKER? So far, I have only been able to edit existing internal coordinate files in their test folder with INTEDIT.exe. How would I get TINKER to run a new z-matrix? I would appreciate any help. Thank you, Rosalie Peck ------=_Part_49245_5380917.1185916252708 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Is it possible to create a z-matrix for TINKER?  So far, I have only been
able to edit existing internal coordinate files in their test folder with
INTEDIT.exe.  How would I get TINKER to run a new z-matrix?

I would appreciate any help. Thank you,
Rosalie Peck
------=_Part_49245_5380917.1185916252708-- From owner-chemistry@ccl.net Wed Aug 1 15:48:00 2007 From: "Jeff Nauss jnauss#%#accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for August and September Message-Id: <-34842-070801111934-23175-C4WQPSe/VkUrw2mPduGHwQ##server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Wed, 1 Aug 2007 08:19:12 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss ~~ accelrys.com] Accelrys Inc. are holding the following training workshops during August and September. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Cost for the on-line presentations is $175 per three hour session for all customers. ON-LINE TRAINING Introduction to Discovery Studio 2 Aug (7am PDT) Catalyst Migration 8 Aug (4pm BST) Insight II to Discovery Studio Migration 15 Aug (7am PDT) Introduction to Materials Studio 21 Aug (4pm BST) Scripting in Materials Studio 22 Aug (4pm BST) Introduction to Discovery Studio 5 Sept (4pm BST) Insight II to Discovery Studio Migration 6 Sept (4pm BST) Sequence Analysis for Homology Modeling 18 Sept (4pm BST) Protein Homology Modeling in Discovery Studio 19 Sept (4pm BST) Simulations in Discovery Studio (Parts 1&2) 20-21 Sept (4pm BST) Docking & Scoring in Discovery Studio 24 Sept (4pm BST) De Novo Design with Discovery Studio 25 Sept (4pm BST) Catalyst to Discovery Studio Migration 26 Sept (4pm BST) Pharmacophore Modeling with Discovery Studio (Parts 1&2) 27-28 Sept (4pm BST) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html. Questions regarding scheduling and content should be directed to workshops-#-accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Wed Aug 1 16:23:00 2007 From: "ss537^drexel.edu" To: CCL Subject: CCL: software for equipotential lines ? Message-Id: <-34843-070801145723-14000-WLZe+C70y5bqVHAbWXc0fQ _ server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 01 Aug 2007 14:56:54 -0400 MIME-Version: 1.0 Sent to CCL by: [ss537(!)drexel.edu] Hey Martin Try using XMgrace, it is has excellent GUI. Cheers Sriraj SRIRAJ SRINIVASAN PhD STUDENT DEPARTMENT OF CHEMICAL AND BIOLOGICAL ENGINEERING DREXEL UNIVERSITY, PHILADELPHIA,PA. PHONE: 215-895-5938 ----- Original Message ----- > From: "Martin Graf graf[#]mpi-muelheim.mpg.de" Date: Wednesday, August 1, 2007 8:12 am Subject: CCL: software for equipotential lines ? > > Sent to CCL by: Martin Graf [graf^mpi-muelheim.mpg.de] > Michael Shokhen shokhen]=[mail.biu.ac.il wrote: > > > > I would appreciate if somebody can address me to a graphical > > software (for Windows) for equipotential lines building > > ( presentation of 2D potential surface, E(x,y)). > > The feature of my data points, E(x,y), is that X and Y coordinates > > are chaotically distributed over the (X,Y) plane, so E(x,y) > cannot be organized in a regular rectangular grid (table with rows > and columns enumerated according to fixed X and Y values, so Excel > graphical tools > > are usless here. > > Have you considered using gnuplot? It is not > the most pretty interface ever, but it does a > good job if you have weird data formats. > > Regards, > > Martin > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the [a] sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Wed Aug 1 17:49:00 2007 From: "Christoph Steinbeck er[a]doktor-steinbeck.de" To: CCL Subject: CCL: Workflow management/web services software Message-Id: <-34844-070801145416-12309-yc3kdNZmuIAUo7L7frxFSw^-^server.ccl.net> X-Original-From: Christoph Steinbeck Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 01 Aug 2007 20:01:23 +0200 MIME-Version: 1.0 Sent to CCL by: Christoph Steinbeck [er|a|doktor-steinbeck.de] Andrew, are you aware of the CDK-Taverna project (http://almost.cubic.uni-koeln.de/cdk/cdk_taverna/)? It's a subproject of CDK. Certainly not production ready but worth a try. Knime also encapsulates CDK, so may want to give both a try. With CDK-Taverna, you are completely on the free software side. Cheers, Christoph Steinbeck Andrew Colasanti acolasanti*gmail.com wrote: > Sent to CCL by: "Andrew Colasanti" [acolasanti.-#-.gmail.com] > I am looking into workflow management software and wanted to know > about experiences and suggestions. The three that I am thinking about > are > > 1) Taverna (taverna.sourceforge.net) > 2) Knime (www.knime.org) > 3) Kepler (kepler-project.org) > > I also know about Pipeline Pilot from SciTegic/Accelrys but the cost > is prohibitive. > > I am also interested in the use of CDK and Openbabel within the > software. The projects will be chem-/bioinformatics based. > > Thanks in advance > > Andrew> > > -- PD Dr. Christoph Steinbeck Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From owner-chemistry@ccl.net Wed Aug 1 18:39:00 2007 From: "LI Daobing lidaobing#gmail.com" To: CCL Subject: CCL: input files for TINKER Message-Id: <-34845-070801182956-20524-eNfTnMjv7ml13FVR/qESnA]-[server.ccl.net> X-Original-From: "LI Daobing" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 2 Aug 2007 04:49:11 +0800 MIME-Version: 1.0 Sent to CCL by: "LI Daobing" [lidaobing]|[gmail.com] On 8/1/07, Rosalie Peck rosaliepeck : gmail.com wrote: > Is it possible to create a z-matrix for TINKER? So far, I have only been > able to edit existing internal coordinate files in their test folder with > INTEDIT.exe. How would I get TINKER to run a new z-matrix? > > I would appreciate any help. Thank you, > Rosalie Peck > $ intxyz ############################################################################## ############################################################################## ## ## ## TINKER --- Software Tools for Molecular Design ## ## ## ## Version 4.2 June 2004 ## ## ## ## Copyright (c) Jay William Ponder 1990-2004 ## ## All Rights Reserved ## ## ## ############################################################################## ############################################################################## Enter Internal Coordinate File Name : Interrupt -- LI Daobing From owner-chemistry@ccl.net Wed Aug 1 19:13:00 2007 From: "Prema Mallipeddi plmallip_-_mail.uh.edu" To: CCL Subject: CCL: Autodock solvation parameters and other changes for Zn2+ enzyme Message-Id: <-34846-070801184534-30003-Yxw+TbICoolYACzTpYLSPQ{:}server.ccl.net> X-Original-From: "Prema Mallipeddi" Date: Wed, 1 Aug 2007 18:45:31 -0400 Sent to CCL by: "Prema Mallipeddi" [plmallip|mail.uh.edu] Dear all, I have recently started using Autodock 3.0.5, along with AutoDockTools. My protein is a metalloenzyme with zinc in the active site. I want to change partial charges of zn2+, which i can do it in pdbqs file. But, what about solvation parameters? Does anyone have, or know where to get, the solvation parameters for Zn+2? What are other important changes I need to make before submitting a docking job for a metalloenzyme with Zn. It would be of great help, if anyone of you can give me suggestions/references where I can a solution in this regard.Thankyou for you time. warm regards, Prema. From owner-chemistry@ccl.net Wed Aug 1 22:44:01 2007 From: "Wibke Sudholt wibke-*-oci.uzh.ch" To: CCL Subject: CCL: Workflow management/web services software Message-Id: <-34847-070801174716-29902-7PsYfBPBEsHUvUKgHqKZRw+*+server.ccl.net> X-Original-From: Wibke Sudholt Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Wed, 01 Aug 2007 23:09:30 +0200 Mime-version: 1.0 Sent to CCL by: Wibke Sudholt [wibke~~oci.uzh.ch] Dear Andrew, You might be interested in the Chemomentum project (http://www.chemomentum.org/), which is targeting the field you are looking for. If you are interested, I can provide you more information. Best regards, Wibke -- Dr. Wibke Sudholt University of Zurich Switzerland wibke]_[oci.uzh.ch On 8/1/07 5:42 PM, "Andrew Colasanti acolasanti*gmail.com" wrote: > > Sent to CCL by: "Andrew Colasanti" [acolasanti.]_[.gmail.com] > I am looking into workflow management software and wanted to know > about experiences and suggestions. The three that I am thinking about > are > > 1) Taverna (taverna.sourceforge.net) > 2) Knime (www.knime.org) > 3) Kepler (kepler-project.org) > > I also know about Pipeline Pilot from SciTegic/Accelrys but the cost > is prohibitive. > > I am also interested in the use of CDK and Openbabel within the > software. The projects will be chem-/bioinformatics based. > > Thanks in advance > > Andrew> > >