From chemistry-request@server.ccl.net Tue Dec 18 06:25:48 2001 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBIBPlU28173 for ; Tue, 18 Dec 2001 06:25:47 -0500 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id MAA22355; Tue, 18 Dec 2001 12:22:23 +0100 (MET) for Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id MAA07962; Tue, 18 Dec 2001 12:25:19 +0100 (MET) for chemistry@ccl.net Date: Tue, 18 Dec 2001 12:25:19 +0100 (MET) Message-Id: <200112181125.MAA07962@mach.vub.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: RMS on atoms position calculation ? X-Mailer: Webmail ULB v2.0 Hello everyone, I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ? Thank's in advance. Pierre Mignon PhD student in the VUB. From chemistry-request@server.ccl.net Tue Dec 18 09:08:06 2001 Received: from myamlak.ch.uj.edu.pl ([149.156.71.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBIE80U30664 for ; Tue, 18 Dec 2001 09:08:01 -0500 Received: from localhost (borowski@localhost) by myamlak.ch.uj.edu.pl (8.9.3/8.9.3) with ESMTP id PAA11775; Tue, 18 Dec 2001 15:02:38 +0100 (MET) Date: Tue, 18 Dec 2001 15:02:38 +0100 (MET) From: Tomasz Borowski X-Sender: borowski@myamlak.ch.uj.edu.pl To: Pierre Mignon cc: chemistry@ccl.net Subject: Re: CCL:RMS on atoms position calculation ? In-Reply-To: <200112181125.MAA07962@mach.vub.ac.be> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try Quatfit available at CCL.net Best regards, Tomek > Hello everyone, > I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ? > Thank's in advance. > Pierre Mignon > PhD student in the VUB. From chemistry-request@server.ccl.net Tue Dec 18 10:34:23 2001 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBIFYMU32241 for ; Tue, 18 Dec 2001 10:34:22 -0500 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id QAA17729 for ; Tue, 18 Dec 2001 16:32:34 +0100 (MET) Message-ID: <3C1F6274.AFFC729A@fy.chalmers.se> Date: Tue, 18 Dec 2001 16:36:20 +0100 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: ViPA or similar programs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I'm interested in programs like ViPA which perform vibration vector projection analysis. Any other suggestions?? (preferrably for Linux or Windows environments) best regards /Patrik -- Patrik Johansson Scientist Materials Physics Chalmers University of Technology 412 96 Goteborg SWEDEN patrikj@fy.chalmers.se http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Tue Dec 18 11:31:28 2001 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBIGUIU00900 for ; Tue, 18 Dec 2001 11:30:18 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id RAA12326; Tue, 18 Dec 2001 17:29:43 +0100 (MET) for Received: from vub.ac.be (algcpc5.vub.ac.be [134.184.24.95]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id RAA00262; Tue, 18 Dec 2001 17:29:49 +0100 (MET) for Message-ID: <3C1F6F2A.9090908@vub.ac.be> Date: Tue, 18 Dec 2001 17:30:34 +0100 From: Pierre Mignon User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: RMS on atoms position calculation Content-Type: multipart/alternative; boundary="------------050206040408050703030502" --------------050206040408050703030502 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello everyone, i'd like to thank some CCLers for their answers upon a program for RMS on atoms position calculation. Here are the answers. Pierre Mignon ------------------------------------------------------- Try MOLMOL: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ Best regards, Andrus ------------------------------------------------------- On Tue, 18 Dec 2001, Pierre Mignon wrote: >>Hello everyone, >>I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ? >>Thank's in advance. > g_confrms is part of gromacs www.gromacs.org but you cannot get it separate. I'm sure someone has a server out there somewhere... Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------------------------------- Hi, >> I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ? > in the CCL archives is such a program, called "quatfit" (the fitting is done using quaternions). It is a command line driven C program, you have to compile yourself. Input files have to be in xmol format. The documentation covers all this. BTW, quatfit has been programmed by J.Labanowsky, the CCL administrator. Regards, Anselm -- _______________________________________________________________________ Anselm Horn, Dipl. Chem. Univ. Anselm.Horn@ccc.uni-erlangen.de ___ / __| ___ Computer Chemie Centrum | / ___ / __| | | / __|| / Naegelsbachstrasse 25 \ \__ | / | | D-91025 Erlangen \___|| | \ \__ Deutschland / Germany \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 \___| http://www.ccc.uni-erlangen.de/clark/horn/index.html _______________________________________________________________________ ------------------------------------------------------- Try Quatfit available at CCL.net Best regards, Tomek ------------------------------------------------------- Dear Pierre, If I remember well Andrew Martin's ProFit can calculate the rmsd between two structures (both small molecules and proteins). It is free for academics and you should be able to download it from: http://www.bioinf.org.uk/ (got to Software and then ProFit). It was written for proteins but I have used it in the past for ligands only. Good luck, Irilenia ------------------------------------------------------- Dear Pierre, try Tinkers superpose ! Thomas Strassner ------------------------------------------------------- Hi, So, you can use GopenMol or Moilview to do it. I think GopenMol is the better one... Pascal ------------------------------------------------------- Dear Pierre, why don't you try our "Server for Pairwise Superposition of Protein 3D Structures and Analysis of Conformational Changes" at : http://www.ucmb.ulb.ac.be/~ocha/wwwsup1/wwwsup.cgi Bye, L. ------------------------------------------------------- Does someone know how to get such a program freely ? MOLMOL http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ ------------------------------------------------------- ------------------------------------------------------- ------------------------------------------------------- ------------------------------------------------------- ------------------------------------------------------- ------------------------------------------------------- --------------050206040408050703030502 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 
Hello everyone, i'd like to thank some CCLers for their answers upon a program for RMS on atoms position calculation. Here are the answers.
Pierre Mignon


-------------------------------------------------------
Try MOLMOL:
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

Best regards,

Andrus

-------------------------------------------------------
On Tue, 18 Dec 2001, Pierre Mignon wrote:


>Hello everyone,
>I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ?
>Thank's in advance.

g_confrms is part of gromacs www.gromacs.org
but you cannot get it separate.

I'm sure someone has a server out there somewhere...

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel@xray.bmc.uu.se	spoel@gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++




-------------------------------------------------------
Hi,


> I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ?


in the CCL archives is such a program, called "quatfit" (the fitting is done using quaternions).
It is a command line driven C program, you have to compile yourself.
Input files have to be in xmol format.
The documentation covers all this. BTW, quatfit has been programmed by J.Labanowsky, the CCL administrator.

Regards,

Anselm



--
_______________________________________________________________________
Anselm Horn, Dipl. Chem. Univ.          Anselm.Horn@ccc.uni-erlangen.de
  ___
 / __|        ___                               Computer Chemie Centrum
| /     ___  / __|
| |    / __|| /                                   Naegelsbachstrasse 25
\ \__ | /   | |                                        D-91025 Erlangen
 \___|| |   \ \__                                 Deutschland / Germany
      \ \__  \___|    Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565
       \___|
       http://www.ccc.uni-erlangen.de/clark/horn/index.html
_______________________________________________________________________






-------------------------------------------------------
Try Quatfit available at CCL.net

Best regards,
Tomek





-------------------------------------------------------
Dear Pierre,

If I remember well Andrew Martin's ProFit can calculate the rmsd between
two structures (both small molecules and proteins). It is free for
academics and you should be able to download it from:
  http://www.bioinf.org.uk/
(got to Software and then ProFit).

It was written for proteins but I have used it in the past for ligands
only.

Good luck,

Irilenia





-------------------------------------------------------
Dear Pierre,


try Tinkers superpose !


Thomas Strassner


-------------------------------------------------------
Hi, 

So, you can use GopenMol or Moilview to do it. I think GopenMol is the
better one...
Pascal
-------------------------------------------------------
Dear Pierre,

why don't you try our "Server for Pairwise Superposition of Protein 3D
Structures and Analysis of Conformational Changes" at :

http://www.ucmb.ulb.ac.be/~ocha/wwwsup1/wwwsup.cgi

Bye,

L.
-------------------------------------------------------
Does someone know how to get such a program freely ?

MOLMOL
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
---------------------------
----------------------------

-------------------------------------------------------

-------------------------------------------------------

-------------------------------------------------------

-------------------------------------------------------

-------------------------------------------------------

--------------050206040408050703030502-- From chemistry-request@server.ccl.net Tue Dec 18 17:03:17 2001 Received: from BRASS.metals.hope.edu ([198.110.98.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fBIM3HU06740 for ; Tue, 18 Dec 2001 17:03:17 -0500 Received: from hope.edu ([198.110.98.17]) by BRASS.metals.hope.edu (NAVGW 2.5.1.13) with SMTP id M2001121817025621446 for ; Tue, 18 Dec 2001 17:02:56 -0500 Received: from [132.249.68.162] (polik@hope.edu); Tue, 18 Dec 2001 17:02:56 -0500 X-WM-Posted-At: hope.edu; Tue, 18 Dec 01 17:02:56 -0500 Message-Id: <5.1.0.14.2.20011218133729.01fa5930@webmail.hope.edu> X-Sender: polik@webmail.hope.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 18 Dec 2001 14:03:43 -0800 To: chemistry@ccl.net From: "William F. Polik" Subject: Useful RedHat Linux / Computational Chemistry Resources Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed In response to various requests, I want to call attention to a series of support pages that assist in the installation of computational chemistry software on Red Hat Linux 6.X and 7.X systems. These instructions are very straightforward to implement (every command to be typed is explicitly specified), and they contain all necessary links on how to obtain the software. * GAMESS installation instructions for Linux http://www.webmo.net/support/gamess_linux.html * MOPAC 7 installation instructions for Linux http://www.webmo.net/support/mopac_linux.html * Gaussian 98 installation instructions for Linux http://www.webmo.net/support/g98_linux.html * Portland Group F77 compiler installation instructions for Linux (required for Gaussian 98) http://www.webmo.net/support/pgf77.html Instructions for installing and configuring Red Hat Linux 7.X are also given. In additional to documenting the installation process, they describe how to configure various services (telnet, ftp, ssh/sftp, apache, samba, sendmail, pop3/imap). The new security models incorporated into Red Hat Linux are also explained (ipchains firewall, xinet.d, hosts.allow/hosts.deny). * RedHat Linux 7.X installation instructions http://www.webmo.net/support/linux72.html Enjoy! ================================ Dr. William F. Polik Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik@hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 On sabbatical leave 9/01-6/02: University of California, San Diego San Diego Supercomputer Center, MC 0505 9500 Gilman Drive La Jolla, CA 92093-0505 tel: 858-822-3610 fax: 858-534-5113 ================================ From chemistry-request@server.ccl.net Tue Dec 18 18:48:32 2001 Received: from nikias.cc.uoa.gr ([195.134.68.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBINmVU09141 for ; Tue, 18 Dec 2001 18:48:32 -0500 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id BAA11936 for ; Wed, 19 Dec 2001 01:48:09 +0200 (EET) Date: Wed, 19 Dec 2001 01:48:09 +0200 (EET) From: Ioannis Kerkines To: chemistry@ccl.net Subject: 20 years of history through Usenet Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Not exactly chemistry-related, but still very very interesting, Google has put down a very nice page with memorable Usenet postings since 1981, e.g. the postings of Tim Berners-Lee for WWW, Marc Andreesen for Mosaic and Netscape, Linus Torvalds for Linux, etc. http://www.google.com/googlegroups/archive_announce_20.html Merry Christmas Ioannis