From chemistry-request@server.ccl.net Fri Sep 21 04:55:03 2001 Received: from rbadb2.rbacpxclu.bas.roche.com ([196.3.50.241]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8L8t3118121 for ; Fri, 21 Sep 2001 04:55:03 -0400 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01K8LGZ0VY8W90SR47@Roche.COM> for chemistry@ccl.net; Fri, 21 Sep 2001 10:52:21 +0200 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01K8LGYUY9Z490SQEU@Roche.COM>; Fri, 21 Sep 2001 10:52:09 +0200 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Fri, 21 Sep 2001 10:53:48 +0200 Content-return: allowed Date: Fri, 21 Sep 2001 10:53:47 +0200 From: "Borosy, Andras {Basi~Basel}" Subject: RE: Exceed 3D 6.1 To: "'Don Key'" , chemistry@ccl.net Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5201E9AA6D@rbamsem3.bas.roche.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8L8t3118126 Dear Don, > > I am a user of software that can be emulated using > Exceed and Exceed 3D. However, these pieces of > software are very expensive. I hope I am not > completely out of line (and I apologize if I am), but > I am having a hard time finding funding. We have an > SGI that was donated, but with out a monitor. > Therefore, I am trying to emulate the openGL. I have > found Exceed 6.1, but I also need Exceed 3D 6.1. I > would greatly appreciate it if someone could make > available to me Exceed 3D 6.1 or any version that you > may have. Again, sorry if this in appropriate. Thank > you everyone. Connect to your SGI to any PC having linux (with the best monitor and configuration that you can afford)! After you can use your PC as a terminal of SGI, in addition you will be enabled to use the vast list of chemical applicatons run on linux. See, http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html Bye, András Borosy From chemistry-request@server.ccl.net Fri Sep 21 05:04:25 2001 Received: from electre.pasteur.fr ([157.99.64.120]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8L94O118723 for ; Fri, 21 Sep 2001 05:04:25 -0400 Received: from pasteur.fr (xiii.bis.pasteur.fr [157.99.90.14]) by electre.pasteur.fr (8.11.6/8.11.6) with ESMTP id f8L94LM197695; Fri, 21 Sep 2001 11:04:21 +0200 (CEST) Sender: tru@pasteur.fr Message-ID: <3BAB0294.411FFE37@pasteur.fr> Date: Fri, 21 Sep 2001 11:04:20 +0200 From: Tru Huynh Organization: Institut Pasteur X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.3-SGI_XFS_1.0.1 i686) X-Accept-Language: en MIME-Version: 1.0 To: "Xiang(Simon) Wang" CC: CCL Subject: Re: CCL:CHARMM Trajectory Analysis References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Xiang(Simon) Wang" wrote: > > Dear CCLers: > > Can someone give me some hints about using COORdinates DYNAmics to > calculate the atomic average RMSD? Any help is appreciated. > Checkout this fine tutorial: http://www.ch.embnet.org/MD_tutorial/index.html section III Analysis of a MD simulation section IV CHARMM exercise 1 .... http://www.ch.embnet.org/MD_tutorial/pages/CHARMM.Exercise1.html and the input file: http://www.ch.embnet.org/MD_tutorial/Exercises/exercise1a/input/md_anal.inp Regards, Tru PS don't forget to post a summary :) -- Dr Tru Huynh | Bioinformatique Structurale mailto:tru@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France From chemistry-request@server.ccl.net Fri Sep 21 06:06:40 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8LA69121275 for ; Fri, 21 Sep 2001 06:06:40 -0400 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Fri, 21 Sep 2001 11:05:14 +0100 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A667D90@GABRIELLE> From: "Robinson, James" To: "'David Gallagher'" , chemistry@ccl.net Subject: RE: The PM5 method? Date: Fri, 21 Sep 2001 11:05:12 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Does PM5 treat amides and sulphonamides better than AM1 or PM5? -----Original Message----- From: David Gallagher [mailto:dgallagher@cachesoftware.com] Sent: Tuesday, September 11, 2001 8:41 PM To: chemistry@ccl.net Subject: CCL:The PM5 method? Dr James Stewart (author of MOPAC) gave a presentation on PM5 at the Chicago ACS on August 28, 2001. He stated that PM5, now includes ALL main group elements in one method, adding Li, Be, B, Na, Mg, K, Ca, etc. PM5 is also claimed to be significantly more accurate than PM3 or AM1 for heats of formation. However, the actual improvement in accuracy varies by element. The average unweighted errors in absolute heats of formation (kcal/mol) for each method compared to experiment is approximately as shown below. The averages are based on all elements previously published by Stewart for PM3 and AM1, and for all main group elements for PM5. Of course, relative errors are typically much smaller. AM1 16.4 kcals/mol PM3 20.4 kcals/mol PM5 5.6 kcals/mol (preliminary results) PM5 works with the COSMO solvation field and on systems of up to 20,000 atoms when using the linear scaling option. Fujitsu is currently testing a beta version of PM5 at present. The PM5 method will be available in CAChe at the end of this month (September), and also in a new release of MOPAC 2002 in the near future, when more information should become available. David Gallagher Fujitsu ( www.cachesoftware.com/cache5/ ) At 06:36 AM 9/11/2001 -0700, Mark A. Thompson wrote: Has the new "PM5" method been described in the literature anywhere? Mark http://www.planaria-software.com From chemistry-request@server.ccl.net Fri Sep 21 06:08:29 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8LA8T121310 for ; Fri, 21 Sep 2001 06:08:29 -0400 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Fri, 21 Sep 2001 11:07:34 +0100 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A667D91@GABRIELLE> From: "Robinson, James" To: "'David Gallagher'" , "'chemistry@ccl.net'" Subject: RE: The PM5 method? Date: Fri, 21 Sep 2001 11:07:25 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" ooops, I meant does PM5 treat amides and sulfonamides better than Am1 and Pm3. James -----Original Message----- From: Robinson, James Sent: Friday, September 21, 2001 11:05 AM To: 'David Gallagher'; chemistry@ccl.net Subject: RE: The PM5 method? Does PM5 treat amides and sulphonamides better than AM1 or PM5? -----Original Message----- From: David Gallagher [mailto:dgallagher@cachesoftware.com] Sent: Tuesday, September 11, 2001 8:41 PM To: chemistry@ccl.net Subject: CCL:The PM5 method? Dr James Stewart (author of MOPAC) gave a presentation on PM5 at the Chicago ACS on August 28, 2001. He stated that PM5, now includes ALL main group elements in one method, adding Li, Be, B, Na, Mg, K, Ca, etc. PM5 is also claimed to be significantly more accurate than PM3 or AM1 for heats of formation. However, the actual improvement in accuracy varies by element. The average unweighted errors in absolute heats of formation (kcal/mol) for each method compared to experiment is approximately as shown below. The averages are based on all elements previously published by Stewart for PM3 and AM1, and for all main group elements for PM5. Of course, relative errors are typically much smaller. AM1 16.4 kcals/mol PM3 20.4 kcals/mol PM5 5.6 kcals/mol (preliminary results) PM5 works with the COSMO solvation field and on systems of up to 20,000 atoms when using the linear scaling option. Fujitsu is currently testing a beta version of PM5 at present. The PM5 method will be available in CAChe at the end of this month (September), and also in a new release of MOPAC 2002 in the near future, when more information should become available. David Gallagher Fujitsu ( www.cachesoftware.com/cache5/ ) At 06:36 AM 9/11/2001 -0700, Mark A. Thompson wrote: Has the new "PM5" method been described in the literature anywhere? Mark http://www.planaria-software.com From chemistry-request@server.ccl.net Fri Sep 21 09:19:28 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8LDJQ124789 for ; Fri, 21 Sep 2001 09:19:26 -0400 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id f8LDJLb91944; Fri, 21 Sep 2001 15:19:22 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Fri, 21 Sep 2001 15:19:21 +0200 (EET) From: Arvydas Tamulis To: cc: Jelena Tamuliene , Subject: DFT-TD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, Would you please advise free DFT-TD program calculating charge redistribution in various excited states and oscillator strengths. Better if this programm should be parallelized (we have heterogenic cluster Alpha-XP1000+6xAMD(1.2GHz,512Mb,40Gb). Thanking your in advance. Best regards, Arvydas Tamulis c/o Vykintas Tamulis and Jelena Tamuliene ******************************** Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Phone: +(370-2)-778743 From chemistry-request@server.ccl.net Fri Sep 21 17:00:43 2001 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8LL0g132666 for ; Fri, 21 Sep 2001 17:00:42 -0400 Received: from daveg.cachesoftware.com (DAVEG-LIFEBOOK.cachesoftware.com. [192.168.110.12]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id f8LL47N31316; Fri, 21 Sep 2001 14:04:07 -0700 Message-Id: <5.1.0.14.0.20010921131043.02896810@mail.cachesoftware.com> X-Sender: daveg@mail.cachesoftware.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 21 Sep 2001 14:04:34 -0700 To: chemistry@ccl.net From: David Gallagher Subject: RE: The PM5 method? Cc: "Robinson, James" In-Reply-To: <5FD8C12EECBBD4119DD10002B3027B9A667D91@GABRIELLE> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed James, I just ran some quick calculations on N-methylacetamide using PM3 and PM5. Here are the preliminary results without using MOPAC's built-in Amide correction (NOMM). The barrier was determined using the reaction coordinate to rotate around the Carbonyl-Nitrogen bond. PM3 CO-N rotational energy barrier 7.1 kcals PM5 CO-N rotational energy barrier 12.4 kcals Experimental CO-N rotational energy barrier 14 kcals? Also, the nitrogen is flat with PM5 but pyramidal with PM3. I believe that experiment indicates that it should be flat. So far for amides, PM5 seems to be an improvement over PM3. If you can suggest some simple sulphonamides (that will run quickly on my modest home computer) and associated experimental data, I'll try to run them over the weekend. I have been told that the release version of PM5 (in CAChe MOPAC 2002) should be available for evaluation in about 2 weeks. David Gallagher, Fujitsu At 11:07 AM 9/21/2001 +0100, Robinson, James wrote: >ooops, I meant does PM5 treat amides and sulfonamides better than Am1 and >Pm3. > >James > >-----Original Message----- >From: Robinson, James >Sent: Friday, September 21, 2001 11:05 AM >To: 'David Gallagher'; chemistry@ccl.net >Subject: RE: The PM5 method? > > >Does PM5 treat amides and sulphonamides better than AM1 or PM5? > >-----Original Message----- >From: David Gallagher [mailto:dgallagher@cachesoftware.com] >Sent: Tuesday, September 11, 2001 8:41 PM >To: chemistry@ccl.net >Subject: CCL:The PM5 method? > > >Dr James Stewart (author of MOPAC) gave a presentation on PM5 at the Chicago >ACS on August 28, 2001. > >He stated that PM5, now includes ALL main group elements in one method, >adding Li, Be, B, Na, Mg, K, Ca, etc. > >PM5 is also claimed to be significantly more accurate than PM3 or AM1 for >heats of formation. However, the actual improvement in accuracy varies by >element. The average unweighted errors in absolute heats of formation >(kcal/mol) for each method compared to experiment is approximately as shown >below. The averages are based on all elements previously published by >Stewart for PM3 and AM1, and for all main group elements for PM5. Of course, >relative errors are typically much smaller. > >AM1 16.4 kcals/mol >PM3 20.4 kcals/mol >PM5 5.6 kcals/mol (preliminary results) > >PM5 works with the COSMO solvation field and on systems of up to 20,000 >atoms when using the linear scaling option. > >Fujitsu is currently testing a beta version of PM5 at present. The PM5 >method will be available in CAChe at the end of this month (September), and >also in a new release of MOPAC 2002 in the near future, when more >information should become available. > >David Gallagher >Fujitsu ( www.cachesoftware.com/cache5/ > ) > > > >At 06:36 AM 9/11/2001 -0700, Mark A. Thompson wrote: > > > >Has the new "PM5" method been described in the literature anywhere? > >Mark > > > >http://www.planaria-software.com From chemistry-request@server.ccl.net Fri Sep 21 14:00:53 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8LI0r129680 for ; Fri, 21 Sep 2001 14:00:53 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id OAA25135 for ; Fri, 21 Sep 2001 14:00:52 -0400 (EDT) Date: Fri, 21 Sep 2001 14:00:52 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net Subject: Chime and IE 5.5 SP2 announcement (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For your information... Jan ---------- Forwarded message ---------- Date: Wed, 19 Sep 2001 10:50:08 -0700 From: Robert Dickey To: "'chemweb@ic.ac.uk'" Subject: Chime and IE 5.5 SP2 announcement September 19, 2001 MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 Chime and Chime Pro/Microsoft Internet Explorer 5.5 SP2 Update On August 3, we warned our customers and user community that Microsoft had unexpectedly removed support for the plug-in interface and was therefore incompatible with existing versions of Chime and Chime Pro. At the time, we asked our customers to hold off upgrading to Internet Explorer 5.5 SP2 or any later version. We are pleased to announce that we are now confident of delivering a short-term solution to this problem as part of Chime and Chime Pro 2.6 Service Pack 3 (SP3). We expect to release this within the next two weeks. This service pack is designed to work with IE 5.5 SP2, and we expect to be able to extend compatibility to 6.0 at a later date. When used with IE 5.5 SP2 (but not 6.0), this service pack should also have the benefit of fixing the printing problems that have been reported against previous versions of IE 5.5. For the longer term, the Chime team will be continuing to work on architectural changes that will allow Chime to be more independent of the underlying browser technologies. We will release details of these changes on the Chime website once they are firm. Thanks, MDL Chime Product team chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk) From chemistry-request@server.ccl.net Sun Sep 23 17:02:46 2001 Received: from oxygen.chem.nthu.edu.tw (postfix@[140.114.45.223]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8NL2j104916 for ; Sun, 23 Sep 2001 17:02:45 -0400 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id 3962A1CE91; Mon, 24 Sep 2001 05:02:40 +0800 (CST) Date: Mon, 24 Sep 2001 05:02:40 +0800 From: chem@oxygen.chem.nthu.edu.tw To: chemistry@ccl.net Subject: undefined fstat for G98 Message-ID: <20010924050240.B21240@OXYGEN.chem.nthu.edu.tw> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Dear CCLers While I tried to run G98 RevA.7 on Slackware Linux 8.0, the following undefined message appears, g98: error while loading shared libraries: /tmp/pgig98/g98/util.so: undefined symbol: fstat I suspect that this is due to the change to glibc-2.2.3 on Slackware Linux 8.0. Does anyone have some idea to solve this problem? Thanks a lot in advance. Sincerely -- Jen-Shiang Kenny Yu // jsyu@Platinum.chem.nthu.edu.tw Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN From chemistry-request@server.ccl.net Sun Sep 23 15:29:15 2001 Received: from chem.ufl.edu ([128.227.16.141]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8NJTE104072 for ; Sun, 23 Sep 2001 15:29:15 -0400 Received: from chem.ufl.edu (chem.ufl.edu [128.227.32.141]) by chem.ufl.edu (8.9.1/8.9.1/map) with ESMTP id PAA10111 for ; Sun, 23 Sep 2001 15:29:14 -0400 (EDT) Date: Sun, 23 Sep 2001 15:29:14 -0400 (EDT) From: "Xiang(Simon) Wang" To: CCL Subject: SUMMARY:CHARMM Trajectory Analysis Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: Thanks for all the replys to my question about CHARMM trajectory analysis. The atomic average RMSD is just located at the weighting array of the average coordinates. It is embarrassing that I didn't even know where the weighting array is at the begining and didn't realize the RMSD is in the average coordinates already. Two websites are good for CHARMM users: http://www.psc.edu/general/software/packages/charmm/tutorial/index.html http://www.ch.embnet.org/MD_tutorial/ Following are the summaries of the answers. Thanks again. ------------------------------------------------------------------------ Rick Venable I've appended a script I've used to get the RMSD about the average structure for CA atoms in a protein, and write a .crd file with CA atoms only. The RMSD data is in WMAIN, the last column of real numbers in a .crd file; you can extract the data for plotting vs. the RESID via e.g. grep ' CA ' file.crd | awk '{print $2, $10} > ca-rmsd.dat * NPgT aquaporin 1fgy tetramer; check protein CA movement * stream init-p21.str ! READ RTF/PARAM/PSF/COOR coor copy comp ! REQUIRED FOR ORIENT IN COOR DYNA ! OPEN TRAJECTORY FILES set j 1 set u 21 label tlp open unit @U file read name dyn@J.trj incr u by 1 incr j by 1 if j .le. @N goto tlp ! COMPUTE AVERAGE AND RMSD AFTER ALIGNMENT WITH INITIAL COORDS coor dyna firstu 21 nskip 1000 nunit @N - sele atom % * CA end orient sele atom % * CA end ! WRITE THE CA ATOMS TO A FILE open unit 10 write card name avgcat1.crd write coor card unit 10 sele type CA end * average ca coords, with isotropic fluctuations in wmain * stop -------------------------------------------------------------- Tru Huynh Checkout this fine tutorial: http://www.ch.embnet.org/MD_tutorial/index.html section III Analysis of a MD simulation section IV CHARMM exercise 1 .... http://www.ch.embnet.org/MD_tutorial/pages/CHARMM.Exercise1.html and the input file: http://www.ch.embnet.org/MD_tutorial/Exercises/exercise1a/input/md_anal.inp --------------------------------------------------------------