From chemistry-request@server.ccl.net Sat Mar 24 00:06:09 2001 Received: from mumbai3.mtnl.net.in ([203.94.227.53]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2O55mD26021 for ; Sat, 24 Mar 2001 00:05:51 -0500 Received: from bol.net.in by mumbai3.mtnl.net.in (8.9.1/1.1.20.3/27Mar00-0611PM) id KAA0000028593; Sat, 24 Mar 2001 10:34:21 +0530 (IST) Message-ID: <3ABCDA4C.A11BB0D1@bol.net.in> Date: Sat, 24 Mar 2001 23:03:01 +0530 From: Prashant Desai X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Posting Question on CCL Subject: Is Auotdock self sufficient? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I tried understanding DOCK and I realized that one requires 'MS' from QCPE to generate molecular surfaces. Since I don't have 'MS' can anybody suggest some way out? How about using Autodock? Is it self sufficient or even it requires use of some additional softwares? I am also looking for performance comparison of 'Affinity' from MSI with other docking packages. I have not come across as many references on use of Affinity as those for either DOCK or Autodock. Can anyone send me a list of articles where Affinity has been utilized or even compared with other docking softwares? Thanking in advance. Prashant Desai From chemistry-request@server.ccl.net Sat Mar 24 03:25:23 2001 Received: from vytautas.vdu.lt (mail@[193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2O8PGD26471 for ; Sat, 24 Mar 2001 03:25:18 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 14gjM3-0005FB-00; Sat, 24 Mar 2001 10:24:59 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id KAA12624; Sat, 24 Mar 2001 10:25:00 +0200 (GMT) Message-ID: <3ABBBF53.4BC5527F@vaidila.vdu.lt> Date: Fri, 23 Mar 2001 22:25:39 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Prashant Desai CC: CCL Subject: Re: CCL:Is Auotdock self sufficient? References: <3ABCDA4C.A11BB0D1@bol.net.in> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Desai, AutoDock has almost all software to make docking, with exception : 1. To visualize the structures in PDB (the results) 2.To create PDBQ file for ligand and macromolecule (add charges to PDB format). Of course, here we need some force field to calculate charges ....... The latest thing make the most inconvenience to prepare jobs ... And 'addsol' crashes while converting PDBQ to PDBQS file. Here I've wrote my own win32 application. I don't know about DOCK, but AutoDock have rised some doubts about flexible docking. If anybody has the experience of flexible docking with AotoDock 3.0, it would be nice if one could share his/her comments about that . :) have a good day A.Ziemys Prashant Desai wrote: > I tried understanding DOCK and I realized that one requires 'MS' from > QCPE to generate molecular surfaces. Since I don't have 'MS' can anybody > suggest some way out? > How about using Autodock? Is it self sufficient or even it requires use > of some additional softwares? > I am also looking for performance comparison of 'Affinity' from MSI with > other docking packages. I have not come across as many references on use > of Affinity as those for either DOCK or Autodock. Can anyone send me a > list of articles where Affinity has been utilized or even compared with > other docking softwares? > Thanking in advance. > Prashant Desai > > -= 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 Sat Mar 24 12:40:49 2001 Received: from relay2.scripps.edu ([137.131.200.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2OHenD30060 for ; Sat, 24 Mar 2001 12:40:49 -0500 Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay2.scripps.edu (8.11.0/TSRI-4.0r) with ESMTP id f2OHbli13403; Sat, 24 Mar 2001 09:37:47 -0800 (PST) Received: from goliath (goliath [137.131.108.88]) by goliath.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id JAA2163389; Sat, 24 Mar 2001 09:37:47 -0800 (PST) Date: Sat, 24 Mar 2001 09:37:47 -0800 From: "Garrett M. Morris" To: "art'" cc: Prashant Desai , CCL , "Garrett M. Morris" , Arthur Olson , David Goodsell , Michel Sanner Subject: Announcing AutoDock 3.0.5 GUI: AutoDockTools, ADT In-Reply-To: <3ABBBF53.4BC5527F@vaidila.vdu.lt> Message-ID: MIME-Version: 1.0 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 f2OHenD30061 Dear Prashant, With the release of AutoDockTools, also known as 'ADT', AutoDock has become more self-sufficient than ever. ADT provides a graphical user interface to set up the ligand PDBQ file, the AutoGrid grid maps, the AutoDock docking parameters, the ability to launch docking jobs, and the ability to read in and analyse DLG AutoDock docking log files. You can visualize isocontoured AutoGrid maps for atomic affinity and electrostatice potential, and compute and display molecular surfaces. Babel has been ported into ADT, so its Gasteiger partial atomic charge calculation method is available for small molecules, and there is also the ability to assign Kollman united-atom charges to proteins. Previously, you would have needed SYBYL to do this. You can also assign solvation parameters to a macromolecule, and perform operations like adding hydrogens and merging non-polar hydrogens, or detecting aromatic carbons (necessary for solvation parameters). ADT is free for non-commercial applications, and is available from Art Olson's Molecular Graphics Laboratory web site - click on Python Software Development's "Related links", then "Downloads" http://www.scripps.edu/pub/olson-web/index.html After you have accepted the license agreement and registered (free), click the radio button "Download Python packages" and then click "Start". Currently supported platforms are: SGI IRIX 6.2 or higher, R4000 or better Intel Linux 2 Sun Sun OS 5 Coming soon: Windows Mac OS X 10.0 You can select all the packages you want and the packager will tar everything you need into one downloadable file. Just check the "AutoDockTools" check-box and then click "Select dependent packages". The packager determines any dependencies for you. On Fri, 23 Mar 2001, art' wrote: > Hi Desai, > > AutoDock has almost all software to make docking, with exception : > 1. To visualize the structures in PDB (the results) 2.To create > PDBQ file for ligand and macromolecule (add charges to PDB > format). Of course, here we need some force field to calculate > charges ....... > > The latest thing make the most inconvenience to prepare jobs ... > And 'addsol' crashes while converting PDBQ to PDBQS file. Here Email Ruth Huey if you have problems with "addsol" - her email address is rhuey@scripps.edu; this may have already been fixed in the currently released tar file. > I've wrote my own win32 application. > > I don't know about DOCK, but AutoDock have rised some doubts about > flexible docking. If anybody has the experience of flexible > docking with AotoDock 3.0, it would be nice if one could share > his/her comments about that . :) Take a look at the paper in the Journal of Computational Chemistry comparing Simulated Annealing, Genetic Algorithm and Lamarckian Genetic Algorithm in AutoDock 3.0: Morris, G. M.,  Goodsell, D. S.,  Halliday, R.S.,  Huey, R.,  Hart, W. E.,  Belew, R. K.  and  Olson, A. J.  (1998), J. Computational Chemistry, 19: 1639-1662. "Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function". AutoDock's web site is at: http://www.scripps.edu/pub/olson-web/doc/autodock/ For more information and a list of peer-reviewed publications, click on "References". > > have a good day > A.Ziemys > > > Prashant Desai wrote: > > > I tried understanding DOCK and I realized that one requires 'MS' from > > QCPE to generate molecular surfaces. Since I don't have 'MS' can anybody > > suggest some way out? > > How about using Autodock? Is it self sufficient or even it requires use > > of some additional softwares? > > I am also looking for performance comparison of 'Affinity' from MSI with > > other docking packages. I have not come across as many references on use > > of Affinity as those for either DOCK or Autodock. Can anyone send me a > > list of articles where Affinity has been utilized or even compared with > > other docking softwares? > > Thanking in advance. > > Prashant Desai > > > > > -= 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 Happy docking! Garrett ___ Dr Garrett M. Morris, MA, DPhil The Scripps Research Institute, tel: (858) 784-2292 Dept. Molecular Biology, MB-5, fax: (858) 784-2860 10550 North Torrey Pines Road, email: garrett@scripps.edu La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm