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