From chemistry-request@server.ccl.net Sun Dec 3 12:45:58 2000 Received: from resstor.ndsu.nodak.edu (resstor.ndsu.NoDak.edu [134.129.111.204]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14061 for ; Sun, 3 Dec 2000 12:45:57 -0500 Received: from sud8b.pharm.ndsu.NoDak.edu (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) by resstor.ndsu.nodak.edu (8.9.3/8.9.3) with SMTP id LAA24376; Sun, 3 Dec 2000 11:45:44 -0600 Date: Sun, 03 Dec 2000 11:44:36 -0600 From: "Xin Hu" To: chemistry@ccl.net Subject: AUTODOCK screening Message-ID: <886300398.975843876@sud8b.pharm.ndsu.NoDak.edu> X-Mailer: Mulberry (Win32) [1.3.3, s/n S-398030] X-Authenticated: xin_hu by imap.ndsu.nodak.edu X-Licensed-To: Mulberry User MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I am a newer of CCL and this is my first poster. Hopefully someone will give me a response! My question is about AUTODOCK3.0. 1) How to do screening using autodock? DO I need a special program to prepare the input file of ligand or is there another version of Autodock for screening? 2) Does someone know how to use autodock to deal with the metal in macromolecules such as Zn? If simply adding the Zn in the macrr.pdbqs file, how to define the parameters in the macro.gpf file? what the value such as R and Epsilon should be used? I would be appreciated for your help! Xin Hu College of Pharmacy North Dakota State University Fargo, ND58102 701-231-8298 From chemistry-request@server.ccl.net Sun Dec 3 13:08:17 2000 Received: from erouter1.it-datacntr.louisville.edu (erouter1.it-datacntr.louisville.edu [136.165.1.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA14192 for ; Sun, 3 Dec 2000 13:08:17 -0500 Received: from athena.louisville.edu (athena.louisville.edu [136.165.1.37]) by erouter1.it-datacntr.louisville.edu (Postfix) with ESMTP id D3F1D22E3D for ; Sun, 3 Dec 2000 13:05:59 -0500 (EST) Received: by athena.louisville.edu (Postfix, from userid 14322) id 5B76BBD5; Sun, 3 Dec 2000 13:05:32 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by athena.louisville.edu (Postfix) with ESMTP id 537E3BD2 for ; Sun, 3 Dec 2000 13:05:32 -0500 (EST) Date: Sun, 3 Dec 2000 13:05:32 -0500 (EST) From: Antonio Luiz Noronha To: chemistry@ccl.net Subject: AMBER6 input file Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Can someone please tell me what is the best way to convert a PDB file generated in Macromodel into a AMBER6 PDB file? I'm having some problems. Without reason, the leap, when it reads my structure add lots of new heavy atoms, in positions really weird. Thank you Best Regards Antonio Luiz Oliveira de Noronha - PhD Student/Chem. Dep. Structural Biology - Trent Group J.G. Brown Cancer Center Molecular Modeling Facility University of Louisville Louisville, KY, USA From chemistry-request@server.ccl.net Sun Dec 3 12:20:03 2000 Received: from avfw98.lundbeck.com (firewall.lundbeck.com [130.227.160.11]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA13980 for ; Sun, 3 Dec 2000 12:20:02 -0500 Received: from firewall.lundbeck.com [130.227.160.11] (HELO localhost) by avfw98.lundbeck.com (AltaVista Mail V2.0J/2.0J BL25J listener) id 0000_005d_3a2a_8e77_90d6; Sun, 03 Dec 2000 18:18:31 +0000 Received: from somewhere by smtpxd Sender: torleif@ccl.net Message-ID: <3A2A8B5B.FE4A1644@lundbeck.com> Date: Sun, 03 Dec 2000 19:05:16 +0100 From: Torleif alternative account X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-22 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Digest: Java molecule display and modelling tools. Content-Type: multipart/alternative; boundary="------------354715282B11A7B8B8B97443" --------------354715282B11A7B8B8B97443 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings, I thank for all the great responses I got on my query and I have compiled a list of molecule display and modelling applications on: http://www.torleif.org/computing/ I am still interested in hearing from people who have other tools available and would like to have me test then out. - keep them comming. Regards --- Jan -- Dr. Jan T. Pedersen H. Lundbeck A/S Ottiliavej 9 2500 Valby Copenhagen, Denmark phone : +45 36 44 24 25 ext 2887 email: jatp@lundbeck.com --------------354715282B11A7B8B8B97443 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings,

I thank for all the great responses I got on my query and I have compiled a list of molecule display and modelling applications on:

http://www.torleif.org/computing/

I am still interested in hearing from people who have other tools available and would like to have me test then out. - keep them comming.

                            Regards

                                    --- Jan 

-- 
Dr. Jan T. Pedersen
H. Lundbeck A/S
Ottiliavej 9
2500 Valby
Copenhagen, Denmark

phone : +45 36 44 24 25 ext 2887
email: jatp@lundbeck.com
  --------------354715282B11A7B8B8B97443-- From chemistry-request@server.ccl.net Sun Dec 3 18:09:13 2000 Received: from resstor.ndsu.nodak.edu (resstor.ndsu.NoDak.edu [134.129.111.204]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA15335 for ; Sun, 3 Dec 2000 18:09:12 -0500 Received: from sud8b.pharm.ndsu.NoDak.edu (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) by resstor.ndsu.nodak.edu (8.9.3/8.9.3) with SMTP id RAA26525; Sun, 3 Dec 2000 17:09:09 -0600 Date: Sun, 03 Dec 2000 17:07:52 -0600 From: "Xin Hu" To: "Maneesh Yadav" Subject: thanks: autodock screening Message-ID: <905696678.975863272@sud8b.pharm.ndsu.NoDak.edu> X-Mailer: Mulberry (Win32) [1.3.3, s/n S-398030] X-Authenticated: xin_hu by imap.ndsu.nodak.edu X-Licensed-To: Mulberry User MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Maneesh: Thank you very much for your kind help. I am very appreciate if you send me your scripts. Actually I just want to do a small screening for my own virtual library, which I built with Hyperchem(.hin formate) or PDB formate. If possible I would like to screen the database such as ACD or other. Anyway I think it is easier to entend to database screening, right? I am glad to know you and may need your further help. Thank you again. xin --On Sunday, December 03, 2000, 2:19 PM -0800 "Maneesh Yadav" wrote: > Hi Xin, > I did some screening with autodock, there is no method to do it 'out of > the box' but with some simple shell scripting it is possible...it largely > depends on where your database of molecules is coming from...the rate > limiting step is the assignment of torsions to the ligands which is easier > with the new version of autotors...I'd be hapy to send you my (real > simple) mol2 related scripts if you need it... > > On Sun, 3 Dec 2000, Xin Hu wrote: > >> Hi, >> I am a newer of CCL and this is my first poster. Hopefully someone will give >> me a response! >> My question is about AUTODOCK3.0. >> 1) How to do screening using autodock? DO I need a special program to >> prepare the input file of ligand or is there another version of Autodock for >> screening? >> 2) Does someone know how to use autodock to deal with the metal in >> macromolecules such as Zn? If simply adding the Zn in the macrr.pdbqs file, >> how to define the parameters in the macro.gpf file? what the value such as R >> and Epsilon should be used? >> >> I would be appreciated for your help! >> >> >> Xin Hu >> College of Pharmacy >> North Dakota State University >> Fargo, ND58102 >> 701-231-8298 >> >> >> -= 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 >> >> >> >> >> >