From chemistry-request@server.ccl.net Wed Sep 11 04:38:15 2002 Received: from radon.pc.helsinki.fi (postfix@[128.214.14.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8B8cE314907 for ; Wed, 11 Sep 2002 04:38:14 -0400 Received: by radon.pc.helsinki.fi (Postfix, from userid 522) id 5489E1E692; Wed, 11 Sep 2002 11:38:13 +0300 (EEST) Date: Wed, 11 Sep 2002 11:38:13 +0300 To: chemistry@ccl.net Subject: SUMMARY:HOW TO PLOT NLMO's FROM G98? Message-ID: <20020911083813.GA6968@chem.helsinki.fi> References: <20020830152140.GA8599@chem.helsinki.fi> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20020830152140.GA8599@chem.helsinki.fi> User-Agent: Mutt/1.3.25i From: straka@chem.helsinki.fi (Michal Straka) Question was: is there a simple way how to plot the NLMO (or NBO) orbitals calculated by NBO module in Gaussian98? --------------------------------------------------- Thanks to: Ilaria Ciofini, Michel Patzchke, Jim Kress, Sergio Emanuel, Douglas J. Fox, Juergen Haas, Dave Wilson --------------------------------------------------- HOWTO: a) http://www.cscs.ch/molekel see FAQ. Run Gaussian with the keyworkd "PLOT" in the NBO section. This creates several FORTRAN output files. (Those are NBO's NLMO's etc., it is written inside.) Load the regular Gaussian logfile first. Load the corresponding FORTRAN file (probably rename it first to have the extension .orb) containing the NBO orbital coefficients with nbo orb. Select and display the orbitals as you do for regular orbitals. -Different FORTRAN files contain NBO's NLMO's etc. -Gfprint keyword should be also specified in input. -When reading basis set with Gen keyword and @PATH, it did not work here, but it worked when basis set was given in Gaussian input. b) 1. Run Gaussian with: #P iop(6/7=3) gfinput pop=nboread formcheck=(mo,basis) ... $NBO AO*=CS $END here * is NLMO NBO etc., see NBO manual. 2. unfchk JOB.fchk 3. Run Gaussian with Chk=JOB iop(6/7=3) gfinput guess=(read,only) -This writes desired orbs to output, than one can plot them with Molden or Molekel in the same way as regular orbitals. Michal From chemistry-request@server.ccl.net Wed Sep 11 08:29:59 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BCTw320328 for ; Wed, 11 Sep 2002 08:29:59 -0400 Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id OAA11299; Wed, 11 Sep 2002 14:27:40 +0200 (MEST) for chemistry@ccl.net Date: Wed, 11 Sep 2002 14:27:40 +0200 (MEST) Message-Id: <200209111227.OAA11299@resu1.ulb.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: Visualizing amber output ... X-Mailer: Webmail ULB v2.1 Hello, I am very new in using amber. I have run some minimizations but the analysis of the output doesn't seem so easy (for me, for instance). Does someone knows some free software to be used to visualize/analyze amber outputs ? (Please not for SGI stations) Thank's in advance. Pierre. Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be From chemistry-request@server.ccl.net Wed Sep 11 11:09:30 2002 Received: from rutchem.rutgers.edu ([128.6.1.216]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BF9U324462 for ; Wed, 11 Sep 2002 11:09:30 -0400 Received: from rutchem.rutgers.edu (chem-xterm-68.rutgers.edu [128.6.173.8]) by rutchem.rutgers.edu (8.9.3/8.9.3) with ESMTP id LAA515363 for ; Wed, 11 Sep 2002 11:09:26 -0400 (EDT) Message-ID: <3D7F5D0B.C01406D7@rutchem.rutgers.edu> Date: Wed, 11 Sep 2002 11:11:07 -0400 From: Margaret Czerw X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: input orientation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody, I am doing energy optimization of few simple molecules. I need my final geometry in exactly the same orientation as my input (as opposed to the standard orientation where the molecule is rotated about its center of charge). Is there any way of keeping the original (input) orientation throughout the calculation. Thanks Margaret -- Margaret Czerw Rutgers, the State University of New Jersey Wright-Rieman Laboratories, Chemistry 610 Taylor Road Piscataway, NJ o8854 Phone: 732-445-5164 email: marczerw@rutchem.rutgers.edu http://members.tripod.com/~mczerw/index.html From chemistry-request@server.ccl.net Wed Sep 11 09:36:11 2002 Received: from laplinux.ethz.ch ([129.132.118.136]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BDaA321673 for ; Wed, 11 Sep 2002 09:36:11 -0400 Received: from laplinux.ethz.ch (localhost [127.0.0.1]) by laplinux.ethz.ch (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id g8BDaPub003256; Wed, 11 Sep 2002 15:36:25 +0200 Received: from localhost (acontini@localhost) by laplinux.ethz.ch (8.12.3/8.12.3/Submit) with ESMTP id g8BDaOvK003253; Wed, 11 Sep 2002 15:36:25 +0200 Date: Wed, 11 Sep 2002 15:36:24 +0200 (CEST) From: Alessandro Contini To: Pierre Mignon cc: chemistry@ccl.net Subject: Re: CCL:Visualizing amber output ... In-Reply-To: <200209111227.OAA11299@resu1.ulb.ac.be> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g8BDaB321674 Hello, you can use successfully VMD or gOPENMOl; they are both free software and they run either under windows or linux systems. Actually I had some display problems with VMD 1.8, and with the help of my collegues Dr. Michael Jakusch and Holga Steuber I tried this solution: a. Use ptraij to generate a .crd and a .pdb file from the top file without waterbox info and removing wat residues: ptraj filename.top < ptraj.in ptraj filename.top < ptraj2.in ptraj.in = trajin [crd filename] [number of first frame] [number of last frame] trajout [crd filename] nobox strip :WAT go ptraj2.in = trajin [crd filename] [number of first frame] [number of last frame] trajout [crd filename] nobox strip :WAT go Then load the pdb file as primary file and the trajectory file as secondary file and everything should work. If you want to follow water trajectories then gOPENMOL does everything in the right way: you load the pdb file with box infos and wat and you load then the trajectory file. The limitation of gOPENMOL is that it is mostly a chemical oriented software, and so is not able to do fancy rendering such as ribbons or cartoons. If anybody has worked out any different solution for displaying traj. in VMD please let me know. Best wishes Alessandro Contini Istituto di Chimica Organica, Facoltā di Farmacia Universitā degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Wed, 11 Sep 2002, Pierre Mignon wrote: > Hello, > I am very new in using amber. I have run some minimizations but the analysis of the output doesn't seem so easy (for me, for instance). Does someone knows some free software to be used to visualize/analyze amber outputs ? (Please not for SGI stations) > Thank's in advance. > Pierre. > > Mignon Pierre > PhD student > Free University of Brussel (VUB) > Dienst Algemene Chemie (ALGC) > Pleinlaan, 2 > 1050 Brussels > Belgium > Tel + 32 2 629 35 16 > Fax + 32 2 629 33 17 > e-mail pmignon@vub.ac.be > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Wed Sep 11 09:31:24 2002 Received: from seupp-smtp.amershambiosciences.com ([192.36.117.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BDVN321534 for ; Wed, 11 Sep 2002 09:31:24 -0400 Received: from seupp-ln21.se.apbiotech.com (unverified [193.180.20.124]) by ns.amershambiosciences.com (Rockliffe SMTPRA 5.2.3) with ESMTP id ; Wed, 11 Sep 2002 15:32:20 +0200 Subject: Re: CCL:fluorescence lifetime calculation To: chemistry@ccl.net Cc: ilfir@bgumail.bgu.ac.il X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: "Najeeb Said" Date: Wed, 11 Sep 2002 14:31:14 +0100 X-MIMETrack: Serialize by Router on seuppln21.xynet.net/Server/xynet(Release 5.07a |May 14, 2001) at 2002-09-11 15:33:27 MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Although some semi-empirical methods allow you to predict wavelength of a photon emitted from the excited state (http://www.accelrys.com/cerius2/zindo.html), these methods will not tell you if an efficient non-radiative relaxation pathway to the ground state is present e.g. cis/trans isomerisation or electron transfer. Ab-initio calculations on the excited state are required to determine this and these are computationally expensive. As an example see (Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines; Sanchez-Galvez, A et al; J. Am. Chem. Soc., 122 (12), 2911 -2924, 2000). The calculation of fluorescence lifetime is an even more challenging area. As I mentioned earlier, depopulation of the excited state can occur by via fluorescence, internal conversion, electron transfer and other processes. These competing processes can be described as a series of rate constants i.e. K(depop) = K(fluorescence) + K(non-fluorescence) Where K(non-fluorescence) = K(internal conversion) + K(electron transfer) + K(other pathways). To determine the fluorescent lifetime (1/ Kfluorescence) of a compound, you would need to follow the trajectory of its excited state along a reaction co-ordinate (time). When you consider that a typical organic dye has a fluorescent lifetime in the nanosecond region and a typical timestep in these calculations is in the fentosecond scale (Jolibois, F et al. J. Am. Chem. Soc.; 2000; 122; 5801-5810), the calculation of fluorescent lifetimes of organic dyes is beyond our capabilities. The area of fluorescence modelling is a fascinating, but challenging area. Can you please send a summary of your answers to this list. Regards, Najeeb Said ================= Amersham Biosciences The Maynard Centre Cardiff, UK ilfir@bgumail.bgu .ac.il To: chemistry@ccl.net Sent by: cc: "Computational Subject: CCL:fluorescence lifetime calculation Chemistry List" 10/09/02 09:30 Hello, I am interested in prediction of fluorescence lifetime of organic molecules. Is there any reasonable approach to calculate this value or make approximate estimation. I suppose I may use difference of energies between ground and exited singlet state. Please send on my mail as I am not subscriber. Thank you. Best regards, Ilfir mailto:ilfir@bgumail.bgu.ac.il -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Sep 11 05:14:09 2002 Received: from jeeves.ccdc.cam.ac.uk ([131.111.113.44]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8B9E8316178 for ; Wed, 11 Sep 2002 05:14:08 -0400 Received: from sun14.ccdc.cam.ac.uk ([131.111.113.48] helo=ccdc.cam.ac.uk) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 3.35 #1 (Debian)) id 17p3ZY-0003w5-00; Wed, 11 Sep 2002 10:14:08 +0100 Sender: jaccos@ccl.net Message-ID: <3D7F095C.AC35457F@ccdc.cam.ac.uk> Date: Wed, 11 Sep 2002 10:14:04 +0100 From: Jacco van de Streek Organization: CCDC X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: "Chemistry@ccl.net" CC: Juan Alexander Padron Garcia Subject: Re: CCL:X ray structure needed References: <3D7E1D9B.CA5A404C@fq.uh.cu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Juan Alexander Padron Garcia wrote: > > Dear List: > > I need the X ray structure of several compounds (octene, 2 > methyl-octanal and nonanal) to compare structure optimizacion methods. > Does any could help me? Hi, I used to do calculations on crystal structures of long-chain compounds (n-alkanes) for my PhD, and I soon learned that it its very hard to obtain suitable single crystals / powder data. As a result, not many crystal structures of long-chain compounds have been solved. If the crystal structures you are looking for have been solved, they should be in the Cambridge Structural Database, which is maintained by the institute I now work for. I searched for the following two fragments: CH2-CH2-CH2-CH2-CH2-HC=O and CH2/3-CH2-CH=CH-CH2-CH2/3 There were no hits for the first one. The second fragment returned crystal structures for alkenoic acids and the like, e.g. cis-13-docosenoic acid, oleic acid (both cis) and 1,2,3-tris(trans-9-octadecenoyl)glycerol (trans). Assuming that you need the crystal structures to check the molecular geometries rather than the crystal packings, these molecules should be a start. Be aware of the effect the crystal packing has on the conformation, though: there is no single "correct" solid-state conformation for molecules this flexible. If you do not have access to the Cambridge Structural Database, please contact mailto:support@ccdc.cam.ac.uk for information on how to obtain the co-ordinates of a specific crystal structure from the Cambridge Structural Database. Jacco. -- Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge United Kingdom From chemistry-request@server.ccl.net Wed Sep 11 09:47:20 2002 Received: from smtp.web.de ([217.72.192.151]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BDlJ321956 for ; Wed, 11 Sep 2002 09:47:19 -0400 Received: from [145.254.230.176] (helo=christian) by smtp.web.de with smtp (WEB.DE(Exim) 4.75 #2) id 17p7pq-0001f5-00; Wed, 11 Sep 2002 15:47:14 +0200 From: Christian Rummey To: chemistry@ccl.net Date: Wed, 11 Sep 2002 14:10:19 +0200 X-Priority: 3 (Normal) Message-Id: <42ZQOZYHOJRLVS1YEBLK0LG64QLO.3d7f32ab@christian> Subject: citation: optimum number of components in PLS MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1252" X-Mailer: Opera 6.04 build 1135 Sender: crummey@web.de Dear CCL Members, I have been told (hi Stefan ;), that there is a rule of thumb that the omptimum number of components for a PLS analysis should not exceed 10% of the number of compounds used - or slightly different from that. In fact: I do not want to start a discussion about how one figures out this number, or anything related, the only thing I need ist a _citation_ for this (/such a) rule of thumb. Any ideas? thank you, c. Christian Rummey, Dipl. Chem. Institut fuer Organische Chemie, Universitaet Wuerzburg mailto:rummey@chemie.uni-wuerzburg.de http://www-organik.chemie.uni-wuerzburg.de/~rummey From chemistry-request@server.ccl.net Wed Sep 11 11:49:02 2002 Received: from rutchem.rutgers.edu ([128.6.1.216]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BFn2326496 for ; Wed, 11 Sep 2002 11:49:02 -0400 Received: from rutchem.rutgers.edu (chem-xterm-68.rutgers.edu [128.6.173.8]) by rutchem.rutgers.edu (8.9.3/8.9.3) with ESMTP id LAA501919 for ; Wed, 11 Sep 2002 11:49:02 -0400 (EDT) Message-ID: <3D7F6652.74ABC984@rutchem.rutgers.edu> Date: Wed, 11 Sep 2002 11:50:42 -0400 From: Margaret Czerw X-Mailer: Mozilla 4.76 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: input orientation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody, In my previous message I forgot to specify that I am using Gaussian. I am doing energy optimization of few simple molecules. I need my final geometry in exactly the same orientation as my input (as opposed to the standard orientation where the molecule is rotated about its center of charge). Is there any way of keeping the original (input) orientation throughout the calculation. Thanks Margaret -- Margaret Czerw Rutgers, the State University of New Jersey Wright-Rieman Laboratories, Chemistry 610 Taylor Road Piscataway, NJ o8854 Phone: 732-445-5164 email: marczerw@rutchem.rutgers.edu http://members.tripod.com/~mczerw/index.html From chemistry-request@server.ccl.net Wed Sep 11 13:20:41 2002 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BHKf329148 for ; Wed, 11 Sep 2002 13:20:41 -0400 Received: from attglobal.net (slip-32-101-104-228.in.us.prserv.net[32.101.104.228]) by prserv.net (out4) with SMTP id <2002091117203920406d748se>; Wed, 11 Sep 2002 17:20:40 +0000 Message-ID: <3D7F3645.E99E57E@attglobal.net> Date: Wed, 11 Sep 2002 12:25:41 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Christian Rummey CC: chemistry@ccl.net Subject: Re: CCL:citation: optimum number of components in PLS References: <42ZQOZYHOJRLVS1YEBLK0LG64QLO.3d7f32ab@christian> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There is something in Ponder's QSAR PLS code that gives a relative quality of fit that is related to something similar to (# of data - # of components)/(1-Rcv). John McKelvey Christian Rummey wrote: > Dear CCL Members, > > I have been told (hi Stefan ;), that there is a rule of thumb that the omptimum > number of components for a PLS analysis should not exceed 10% of the > number of compounds used - or slightly different from that. > > In fact: I do not want to start a discussion about how one figures out this > number, or anything related, the only thing I need ist > > a _citation_ for this (/such a) rule of thumb. > > Any ideas? > > thank you, > c. > > Christian Rummey, Dipl. Chem. > Institut fuer Organische Chemie, Universitaet Wuerzburg > mailto:rummey@chemie.uni-wuerzburg.de > http://www-organik.chemie.uni-wuerzburg.de/~rummey > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Sep 11 14:59:31 2002 Received: from phobos.email.Arizona.EDU ([128.196.133.165]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8BIxV331051 for ; Wed, 11 Sep 2002 14:59:31 -0400 Received: from [128.196.114.180] by phobos.email.Arizona.EDU with HTTP; Wed, 11 Sep 2002 11:59:30 -0700 Date: Wed, 11 Sep 2002 20:59:30 +0200 Message-ID: <3D7F38CD00000D64@phobos.email.Arizona.EDU> From: ezojer@email.arizona.edu Subject: moleculer mechanics / molecular dynamics programs To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" User-Agent: UofA Webmail X-Originating-IP: 128.196.114.180 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g8BIxW331052 Hi everyone, So far I have been doing only quantum-mechanical simulations of organic molecules, but in order tu study inter-molecular effects, I need to study the relative orientation of molecules (in amorphous films), the alignment of molecules on substrates .... For that purpose I would like to use molecular mechanics and molecular dynamics calculations. At this point, I wonder, whether I should use a commercial program (and if so, which one - e.g. Cerius from accelrys ???) or a program that is available for free on the net. thanks a lot for your advice, egbert -------------------------------------------------- Egbert Zojer Department of Chemistry The University of Arizona 1306 E. University Blvd. Tucson, Arizona 85721-0041, USA Tel.: ++1/520/626-6514 Fax.: ++1/520/621-8407 -------------------------------------------------- Institut fuer Festkörperphysik Technische Universität Graz, Graz, Austria -------------------------------------------------- From chemistry-request@server.ccl.net Wed Sep 11 20:47:57 2002 Received: from cse.nd.edu (root@[129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8C0lv314684 for ; Wed, 11 Sep 2002 20:47:57 -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 g8C0ljn29027 for ; Wed, 11 Sep 2002 19:47:45 -0500 (EST) Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g8C0lgn28745 for ; Wed, 11 Sep 2002 19:47:42 -0500 (EST) Date: Wed, 11 Sep 2002 19:47:41 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: charmm size Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I tried to compile charmm with different sizes but it gives me the same Maximum number of ATOMS: 25140, and RESidues: 14000. It doesn't matter whether I use xxlarge, large, medium or small. Anyone knows why? Thanks Alice