From chemistry-request@ccl.net Mon Sep 27 04:15:37 2004 Received: from mtagate3.de.ibm.com (mtagate3.de.ibm.com [195.212.29.152]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8R9FZ18015009 for ; Mon, 27 Sep 2004 04:15:36 -0500 Received: from d12nrmr1507.megacenter.de.ibm.com (d12nrmr1507.megacenter.de.ibm.com [9.149.167.1]) by mtagate3.de.ibm.com (8.12.10/8.12.10) with ESMTP id i8R9QJdW090568; Mon, 27 Sep 2004 09:26:19 GMT Received: from sihl.zurich.ibm.com (sihl.zurich.ibm.com [9.4.16.232]) by d12nrmr1507.megacenter.de.ibm.com (8.12.10/NCO/VER6.6) with ESMTP id i8R9QIIs212522; Mon, 27 Sep 2004 11:26:19 +0200 Received: from biolinux.ch (dhcp23-189.zurich.ibm.com [9.4.23.189]) by sihl.zurich.ibm.com (AIX4.3/8.9.3p2/8.9.3) with ESMTP id LAA80408; Mon, 27 Sep 2004 11:26:16 +0200 Message-ID: <4157DCB7.9080101)at(biolinux.ch> Date: Mon, 27 Sep 2004 11:26:15 +0200 From: Antoine Logean Reply-To: al)at(biolinux.ch Organization: biolinux User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en MIME-Version: 1.0 To: HU lihong , chemistry)at(ccl.net Subject: Re: CCL:Protein Mutant Software References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net HU lihong wrote: > Dear all, > > Recently I want to do mutant for a protein. I am very new to this problem. > Could anyone please tell me how to do mutant for protein or where I can > find information on this? Which software can do mutation? > > Thanks a lot, > > Holly > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY)at(ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow)at(nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > you can try the RAMP program suite of Samudrala. (http://software.compbio.washington.edu). It is written in C, very clean, very easy to install, very well documented : a dream. I say this because I waiste time to rewrite thinks that Samudrala has already implemented in 1995 !!!! Other is the MMTK package of Hinsen. Written in python, simply wonderfull for protein manipulation. have fun Antoine From chemistry-request@ccl.net Mon Sep 27 09:35:39 2004 Received: from Princeton.EDU (postoffice02.Princeton.EDU [128.112.130.38]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8REZcqm007906 for ; Mon, 27 Sep 2004 09:35:38 -0500 Received: from smtpserver1.Princeton.EDU (smtpserver1.Princeton.EDU [128.112.129.65]) by Princeton.EDU (8.12.9/8.12.9) with ESMTP id i8REkMid021623 for ; Mon, 27 Sep 2004 10:46:24 -0400 (EDT) Received: from Princeton.EDU (lotus.Princeton.EDU [128.112.81.82]) (authenticated bits=0) by smtpserver1.Princeton.EDU (8.12.9/8.12.9) with ESMTP id i8REkM0w001819 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Mon, 27 Sep 2004 10:46:22 -0400 (EDT) Message-ID: <415827BD.3080907[at]Princeton.EDU> Date: Mon, 27 Sep 2004 10:46:21 -0400 From: Silviu Zilberman User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6a) Gecko/20031029 X-Accept-Language: en-us, en, he MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: optimization with internal coordinates Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I just recently came across a paper by Jon Baker, Alain Kessi and Bernard Delley [J. Chem. Phys. 105(1), 192, (1996): "The generation and use of delocalized internal coordinates in geometry optimization"] that describes an efficient algorithm for geometry optimization in delocalized internal coordinates. One of the references there is to a suite of programs by J. Baker called OPTIMIZE, that carries out that particular algorithm. I could not find on the web any trace of neither the author, nor the computer code. I did find that it was incorporated in two commercial products. 1. Does anyone has a pointer to the author of the code or the code itself? 2. Are there free computer codes that implements that algorithm? 3. Are there free computer codes that implement other internal coordinates optimization, such as redundant internal coordinates method? Any suggestions are greatly appreciated, Silviu. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu, PhD 213 Frick Laboratory, Department of Chemistry, Princeton University Princeton, NJ 08544, USA phone: 609-258-1834 fax: 609-258-6746 silviu[at]Princeton.EDU %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@ccl.net Mon Sep 27 09:46:56 2004 Received: from Princeton.EDU (postoffice02.Princeton.EDU [128.112.130.38]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8REktqm008594 for ; Mon, 27 Sep 2004 09:46:55 -0500 Received: from smtpserver1.Princeton.EDU (smtpserver1.Princeton.EDU [128.112.129.65]) by Princeton.EDU (8.12.9/8.12.9) with ESMTP id i8REvfid029117 for ; Mon, 27 Sep 2004 10:57:41 -0400 (EDT) Received: from Princeton.EDU (lotus.Princeton.EDU [128.112.81.82]) (authenticated bits=0) by smtpserver1.Princeton.EDU (8.12.9/8.12.9) with ESMTP id i8REvf0w007792 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Mon, 27 Sep 2004 10:57:41 -0400 (EDT) Message-ID: <41582A64.80802[at]Princeton.EDU> Date: Mon, 27 Sep 2004 10:57:40 -0400 From: Silviu Zilberman User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6a) Gecko/20031029 X-Accept-Language: en-us, en, he MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: CCL: optimization with internal coordinates Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I just recently came across a paper by Jon Baker, Alain Kessi and Bernard Delley [J. Chem. Phys. 105(1), 192, (1996): "The generation and use of delocalized internal coordinates in geometry optimization"] that describes an efficient algorithm for geometry optimization in delocalized internal coordinates. One of the references there is to a suite of programs by J. Baker called OPTIMIZE, that carries out that particular algorithm. I could not find on the web any trace of neither the author, nor the computer code. I did find that it was incorporated in two commercial products. 1. Does anyone has a pointer to the author of the code or the code itself? 2. Are there free computer codes that implements that algorithm? 3. Are there free computer codes that implement other internal coordinates optimization, such as redundant internal coordinates method? Any suggestions are greatly appreciated, Silviu. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu, PhD 213 Frick Laboratory, Department of Chemistry, Princeton University Princeton, NJ 08544, USA phone: 609-258-1834 fax: 609-258-6746 silviu[at]Princeton.EDU %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%