From chemistry-request@server.ccl.net Sat Nov 2 00:14:21 2002 Received: from web12803.mail.yahoo.com ([216.136.174.38]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gA25ELf09195 for ; Sat, 2 Nov 2002 00:14:21 -0500 Message-ID: <20021102051420.19785.qmail@web12803.mail.yahoo.com> Received: from [61.9.74.249] by web12803.mail.yahoo.com via HTTP; Fri, 01 Nov 2002 21:14:20 PST Date: Fri, 1 Nov 2002 21:14:20 -0800 (PST) From: amor san juan Subject: Re: CCL:Covalent map in Autodock and Autodocktools To: olivier walker , chemistry@ccl.net In-Reply-To: <5.1.1.6.0.20021101151346.00abd2c0@imap.wam.umd.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello Olivier, Im using both AD3 & ADT. In my experience, I encountered no problem when ADT is outputting 'CONNECT' terms in the ligand. This generated ligand.pdbq together w/ macro.pdbqs is processed by mkgpf3 & mkdpf3 to generate GPF and DPF files. Then, these are used as input for autogrid3 then, autodock3. All my results are alright. Regarding your ADT's concern about covalent maps, I suggest you read PMV totorial by Miss Sophie Coon (TSRI) located at autodock website. Perhaps, you can get an idea & instructions from this PMV where ADT is viewed. Hope this helps! Best, Amor San Juan M.Sc. Chem candidate University of the Philippines-Diliman --- olivier walker wrote: > > > Hi, > > > To explore the conformation of a dual domain > protein, I use Autdock and > Autodocktools, making one domain the ligand (I'm > just interested in > rotating 20 bounds for the 6 residues of the linker) > and the other one the > macromolecule. I've several questions regarding > these two programs: > > 1) When I create pdbq files from mol2 files (from > InsightII), I obtrain > completely different files. The file created by > Autodock utility program > mol2topdbq is fine, but the one created by > Autodocktools adds a bunch of > ''CONNECT'' word that autodock3 couldn't understand. > What did I wrong? > > > Thus, I'm using the command line to create input > files to use with > autodock3. The most important issue is that I need > the extremity of my > linker to be stick with the macromolecule. > > 2) How to create a covalent map with Autodock or > Autodocktools? > a) With Autodocktools, I tried to select an > atom on the > macromolecule and then create a covalent map but > when I click on the box > ''use selection'', I always receive the same message > "incorrect ligand file > format-unable to write with Z atom". > > > b) How to create such a covalent map with > Autogrid and how to > specify the 2 atoms I want to be linked? I read the > manual or the tutorial > for these two programs, but this section is not well > documented. > > I will appreciate any help. > > Olivier > > > > > > > > ************************************************** > Olivier WALKER > Department of Chemistry & Biochemistry > University of Maryland > College Park, MD 20742 > USA > ************************************************** > Fax : 301-314-0386 > Phone : 301-405-8710 > E-mail : oliwalk@wam.umd.edu > ************************************************** > > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do you Yahoo!? HotJobs - Search new jobs daily now http://hotjobs.yahoo.com/ From chemistry-request@server.ccl.net Sat Nov 2 12:12:16 2002 Received: from typhoeus.chem.york.ac.uk ([144.32.72.225]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA2HCFR17099 for ; Sat, 2 Nov 2002 12:12:16 -0500 Received: from ysbl.york.ac.uk (onion [144.32.72.165]) by typhoeus.chem.york.ac.uk (8.11.6+Sun/8.11.6) with ESMTP id gA2HFYo13310 for ; Sat, 2 Nov 2002 17:15:34 GMT Sender: chandra@ysbl.york.ac.uk Message-ID: <3DC4076E.623ED360@ysbl.york.ac.uk> Date: Sat, 02 Nov 2002 17:12:14 +0000 From: Chandra Verma X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Help MPI Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi When I run a parallel job using MPI my script looks like rand100 0 rand101 1 charmm rand102 1 charmm rand103 1 charmm now each of the rands is a machine with two processors so if i want to run the same job but over two rand machines utilizing both processors on each instead of a single processor across each of the 4 machines, what do I do. Grateful for any suggestions thanks chandra From chemistry-request@server.ccl.net Sat Nov 2 19:11:30 2002 Received: from dux.ru ([193.125.210.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA30BTw01216 for ; Sat, 2 Nov 2002 19:11:30 -0500 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id gA30Hld1090705 for ; Sun, 3 Nov 2002 03:17:56 +0300 (MSK) (envelope-from dima@xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id gA30Hkqo090704 for chemistry@ccl.net; Sun, 3 Nov 2002 03:17:46 +0300 (MSK) (envelope-from dima@xenon.spb.ru) Received: from goblin (goblin [192.168.3.2]) by shadow (8.9.3/8.9.3/Debian 8.9.3-21) with SMTP id DAA11874 for ; Sun, 3 Nov 2002 03:09:02 +0300 Message-ID: <010d01c282cd$3fc9c6d0$0203a8c0@goblin> From: "Dmitry Rozmanov" To: "CCL" Subject: NWChem Date: Sun, 3 Nov 2002 03:09:16 +0300 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Hi. Does anybody use NVChem? Does it have any advantages over Gamess-US? Thanks. ---Dmitry.