From chemistry-request@server.ccl.net Tue Jul 2 07:26:11 2002 Received: from pizarro.unex.es (root@[158.49.8.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g62BQAu26251 for ; Tue, 2 Jul 2002 07:26:10 -0400 Received: from tajo.unex.es (root@tajo.unex.es [158.49.133.12]) by pizarro.unex.es (8.9.3/8.9.1) with ESMTP id NAA13448 for ; Tue, 2 Jul 2002 13:03:45 +0200 Received: from qohermes.unex.es ([158.49.118.11]) by tajo.unex.es (8.9.3/8.9.1) with ESMTP id NAA09288 for ; Tue, 2 Jul 2002 13:03:45 +0200 X-Authentication-Warning: tajo.unex.es: Host [158.49.118.11] claimed to be qohermes.unex.es Message-Id: <5.1.0.14.2.20020702125818.00a54020@tajo.unex.es> X-Sender: cfernan@tajo.unex.es X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 02 Jul 2002 13:12:02 +0200 To: chemistry@ccl.net From: "Dr. Carlos F. Marcos" Subject: Autodock tools under LINUX (success) Mime-Version: 1.0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi, everybody. I've sent a message a couple of days ago regarding a problem trying to run AutoDockTools under Linux. Thanks so much to all that have answered my question. I could successfully solve the problem just by installing in my system the necessary OpenGL graphic libraries, which come in a packet called Mesa.
On the othe hand, Chris wrote that he found the autodock tools "quite bad and highly unstable". Can anyone suggest an alternative to do flexible docking under Linux? Have a nice day. Carlos.

_____________________________________________________________________= ___
Dr. Carlos Fern=E1ndez Marcos
Departamento de Qu=EDmica Org=E1nica. Facultad de Veterinaria. Universidad d= e Extremadura.
Avenida de las Ciencias s/n. 10071 C=C1CERES (SPAIN)
tel.: 34-927-257158
fax: 34-927-257110
e-mail: cfernan@unex.es
Website:  http://www.unex.es/qoceres/qoceres.htm
________________________________________________________________________
=


From chemistry-request@server.ccl.net Mon Jul 1 23:27:53 2002 Received: from hotmail.com ([64.4.37.180]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g623Rqu12893 for ; Mon, 1 Jul 2002 23:27:52 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 1 Jul 2002 20:27:48 -0700 Received: from 138.23.156.82 by pv2fd.pav2.hotmail.msn.com with HTTP; Tue, 02 Jul 2002 03:27:47 GMT X-Originating-IP: [138.23.156.82] From: "Donald Keidel" To: chemistry@ccl.net Subject: can molecular modeling generate the same x-ray or NMR protein/ligand structures Date: Mon, 01 Jul 2002 20:27:47 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 02 Jul 2002 03:27:48.0121 (UTC) FILETIME=[70274890:01C22178] Hello all, Does anyone know of a review that talks of molecular modeling techniques and their accuracy in predicting known X-ray structures (proteins or small molecules). The review I am dreaming of might look at different programs available today and compare their output to known X-ray or NMR structures of the same protein complexed with ligand or small molecule. Thank you all in advance for your time and energy. Don _________________________________________________________________ Join the world’s largest e-mail service with MSN Hotmail. http://www.hotmail.com From chemistry-request@server.ccl.net Tue Jul 2 03:58:41 2002 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g627wfu19954 for ; Tue, 2 Jul 2002 03:58:41 -0400 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id KAA40324; Mon, 1 Jul 2002 10:01:22 +0200 (CEST) Date: Mon, 1 Jul 2002 10:01:22 +0200 (CEST) Message-Id: <200207010801.KAA40324@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: cfernan@unex.es CC: chemistry@ccl.net In-reply-to: <5.1.0.14.2.20020630210400.00a56030@tajo.unex.es> (cfernan@unex.es) Subject: Re: CCL:Autodock tools under LINUX References: <5.1.0.14.2.20020630210400.00a56030@tajo.unex.es> Indeed it is trivial. libglut.so.3 is part of OpenGL or Mesa, a 3D graphis library. In most linux distributions you have to install it separately. Taken SuSE as an example you would have to install the package mesaglut. Regards, Ingo Brunberg > >
> Hi everyone, Sorry if my question is trivial. I'm having > some trouble getting autodock tools or Pmv to work. When I try to run the > pmv script I get the following error: "ImportError: libglut.so.3: > cannot open shared object file: No such file or directory". I have > no idea if libglut.so.3 is general library of LINUX, or if it's specific > of Phyton or ADT, and I don't know how to solve the problem. Has anyone > solved anything similar? Thanks in advance. Carlos.

>

> ________________________________________________________________________
> Dr. Carlos Fernández Marcos
> Departamento de Química Orgánica. Facultad de Veterinaria. Universidad de > Extremadura.
> Avenida de las Ciencias s/n. 10071 CÁCERES (SPAIN)
> tel.: 34-927-257158
> fax: 34-927-257110
> e-mail: cfernan@unex.es
> Website:  > http://www.unex.es/qoceres/qoceres.htm
> ________________________________________________________________________

>

> From chemistry-request@server.ccl.net Tue Jul 2 18:25:03 2002 Received: from cse.nd.edu (root@[129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g62MP3x12391 for ; Tue, 2 Jul 2002 18:25:03 -0400 Received: from dylan.cse.nd.edu (ako@dylan.cse.nd.edu [129.74.32.170]) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id g62MOxI21015 for ; Tue, 2 Jul 2002 17:24:59 -0500 (EST) Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g62MOvD11417 for ; Tue, 2 Jul 2002 17:24:57 -0500 (EST) Date: Tue, 2 Jul 2002 17:24:57 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: several silly questions about MD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am sorry that I have some simple questions about molecular dynamics using charmm. 1) Should I solvate the protein before minimizing it or after? What's the difference? 2) I am using periodic boundary condition. Do I need to put the image in when I do minimization? 3) What is the difference between equilibration and the actual trajectory production (dynamics or simulation) phase? Is it something to do with update the velocities ( or scaling with the velocity)? 4) How do I set NVT in charmm? I know how to set constant temperature. But I don't know what it means by constant volume. Thanks for your help and I really appreciate your time. Alice From chemistry-request@server.ccl.net Tue Jul 2 21:24:06 2002 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g631O5x27491 for ; Tue, 2 Jul 2002 21:24:05 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g631O5J25666 for ; Tue, 2 Jul 2002 18:24:05 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 27953; Tue, 02 Jul 2002 18:18:48 -0700 (PDT) Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay2.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g631Nxu20553 for ; Tue, 2 Jul 2002 18:23:59 -0700 (PDT) Received: from goliath (goliath [137.131.108.88]) by goliath.scripps.edu (SGI-8.9.3/TSRI-3.0.1) with ESMTP id SAA36740 for ; Tue, 2 Jul 2002 18:23:59 -0700 (PDT) Date: Tue, 2 Jul 2002 18:23:58 -0700 From: "Garrett M. Morris" To: chemistry@ccl.net Subject: Re: CCL:Autodock tools under LINUX (success) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Carlos, I read your post on the CCL about AutoDockTools on Linux. I'm happy you figured out what your problem was with your Operating System. Have you actually tried using AutoDockTools? On Tue, 2 Jul 2002, Dr. Carlos F. Marcos wrote: > > Hi, everybody. I've sent a message a couple of days ago regarding > a problem trying to run AutoDockTools under Linux. Thanks so much > to all that have answered my question. I could successfully solve > the problem just by installing in my system the necessary OpenGL > graphic libraries, which come in a packet called Mesa. On the othe > hand, Chris wrote that he found the autodock tools "quite bad and > highly unstable". Can anyone suggest an alternative to do flexible > docking under Linux? Have a nice day I was curious to know who "Chris" is, your reply to CCL did not explain who he was or which version of AutoDockTools he had used and on which platform. We have never heard from Chris about his experiences, and we would love to hear from him, in particular what gave him the impression that ADT was "quite bad and highly unstable". We have a large number of people using AutoDockTools quite happily here at Scripps and elsewhere around the world. Any feedback is always welcome, so that we can make future releases better. Furthermore, I would appreciate you making a distinction in your discussions in public fora like the CCL, between "AutoDock" and "AutoDockTools" (ADT). AutoDock is a standalone computational package, that does not have, and does not require a GUI to run. It is very stable and well tested. AutoDock has been distributed to more than 1600 sites around the world in the last decade, and there are more than 300 publications in the literature citing its successful use. AutoDock is under active development, and its popularity is continuing to grow. AutoDockTools is a Graphical User Interface (GUI) and is relatively new, having been distributed in just the last couple of years. It is still evolving and being developed, chiefly by Ruth Huey, and builds upon the terrific Python Molecule Viewer (PMV) developed by Michel Sanner, also here at Scripps. The ADT GUI helps to make AutoDock easier to use. AutoDockTools is *not* required to run AutoDock. Even if you cannot get AutoDockTools to run on your particular flavour of operating system, AutoDock will still run without problems, and you can still carry out flexible docking. The User Guide distributed with AutoDock explains in great detail how to do this. I hope this clears up any misconceptions, and I look forward to hearing from you about your posting and experiences, Best wishes, 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