From owner-chemistry@ccl.net Tue Aug 28 02:35:00 2007 From: "immanuel feng feng.immanuel.__.gmail.com" To: CCL Subject: CCL: looking for keyword for new DFT with Gaussian Message-Id: <-35038-070827111125-31405-2WgAoL7VHRIL0sDaSSFbQQ__server.ccl.net> X-Original-From: "immanuel feng" Content-Type: multipart/alternative; boundary="----=_Part_62180_26334737.1188223608013" Date: Mon, 27 Aug 2007 22:06:48 +0800 MIME-Version: 1.0 Sent to CCL by: "immanuel feng" [feng.immanuel ~~ gmail.com] ------=_Part_62180_26334737.1188223608013 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: base64 Content-Disposition: inline SGVsbG8gZXZlcnlvbmUsCiAgQk1LMTCjrE8zTFlQMTEsMTIsIFgzTFlQMTOjrFRQU1NUUFNTMTQg YXJlIHNhaWQgdG8gYmUgaW5jbHVkZWQgaW4gR2F1c3NpYW4wMwpEMDEsIGNvdWxkIGFueWJvZHkg dGVsbCBtZSB3aGVyZSB0byBmaW5kIHRoZSBpbnB1dCBrZXl3b3JkIHRvIHJ1biB0aGVtIHdpdGgK R2F1c3NpYW4/IFRoYW5rIHlvdSBzbyBtdWNoIQo= ------=_Part_62180_26334737.1188223608013 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: base64 Content-Disposition: inline PGRpdj5IZWxsbyBldmVyeW9uZSwgPC9kaXY+CjxkaXY+Jm5ic3A7Jm5ic3A7PGZvbnQgc2l6ZT0i MiI+Qk1LMTCjrE8zTFlQMTEsMTIsIFgzTFlQMTOjrFRQU1NUUFNTMTQgYXJlIHNhaWQgdG8gYmUg aW5jbHVkZWQgaW4gR2F1c3NpYW4wMyBEMDEsIGNvdWxkIGFueWJvZHkgdGVsbCBtZSB3aGVyZSB0 byBmaW5kIHRoZSBpbnB1dCBrZXl3b3JkIHRvIHJ1biB0aGVtIHdpdGggR2F1c3NpYW4/IFRoYW5r IHlvdSBzbyBtdWNoITwvZm9udD48L2Rpdj4K ------=_Part_62180_26334737.1188223608013-- From owner-chemistry@ccl.net Tue Aug 28 04:01:00 2007 From: "Ol Ga eurisco1^^^pochta.ru" To: CCL Subject: CCL:G: To: Thermochemical calculations from Gaussian output file Message-Id: <-35039-070828035706-4915-nGKUu6FoHtOlR+BXQHOw8g * server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 28 Aug 2007 03:57:02 -0400 Sent to CCL by: "Ol Ga" [eurisco1() pochta.ru] To: Thermochemical calculations from Gaussian output file MOLTRAN - a program for molecular structure construction and visualization, vibrations animation, and thermodynamic calculations http://ichem.unn.runnet.ru/tcg/ (FREE !!!) 5. Calculation of thermodynamic properties: - internal energy - enthalpy - entropy - Gibbs free energy - heat capacities (Cv and Cp) - calculation of partition functions (statsums) for the thermodynamic and/or kinetic studies - calculation translational, rotational, and vibrational contributions - manual setting temperature and pressure - calculation of thermodynamic properties in manually defined temperature ranges 6. Taking into account the internal rotation contributions into the thermodynamics using the different approximations for calculation of internal rotation contributions 7. Automatic estimation of the rotation barrier heights using the Fourier transformation of the calculated potentials. From owner-chemistry@ccl.net Tue Aug 28 05:36:01 2007 From: "Jamie Platts platts{=}Cardiff.ac.uk" To: CCL Subject: CCL: Conference in Computational Bio-inorganic Chemistry, Spring 2008 Message-Id: <-35040-070828042934-21397-uJ3bEazzPt7Q5faL5m7DeA*server.ccl.net> X-Original-From: "Jamie Platts" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 28 Aug 2007 09:29:19 +0100 Mime-Version: 1.0 Sent to CCL by: "Jamie Platts" [platts#%#Cardiff.ac.uk] Dear CCL'ers We are pleased to announce that an MGMS Spring Meeting will take place in Cardiff between 31st March and 2nd April 2008, on the topic of Bio-inorganic Chemistry. The following scientists have accepted invitations to present their work at the conference: * Prof. Jaroslav Burda (Prague) * Prof. Paolo Carloni (Trieste) * Dr. Rob Deeth (Warwick) * Dr. Jeremy Harvey (Bristol) * Prof. Fahmi Himo (Stockholm) * Prof. Nigel Richards (Florida) * Prof. Sason Shaik (Jerusalem) * Dr. Sam de Visser (Manchester) In addition, Dr. Nick Besley (Nottingham) will present the MGMS Silver Jubilee Prize lecture and the AGM of the MGMS will be held on 31st March. More information, including costs and registration details, can be found at the following URL: http://theory.chem.cf.ac.uk/~grant/conf/ We hope to see you here in Cardiff next year! Jamie Platts ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts*cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy From owner-chemistry@ccl.net Tue Aug 28 08:15:01 2007 From: "Keith Butler keeeto2000##yahoo.co.uk" To: CCL Subject: CCL:G: run solvent in Gaussian Message-Id: <-35041-070828081219-4867-zuFBt9uH3taLXj6n3FserA^^server.ccl.net> X-Original-From: Keith Butler Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 28 Aug 2007 13:12:10 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Keith Butler [keeeto2000,yahoo.co.uk] This is an error because Gaussian treats H atoms as part of a fragment (OH,CH,SH etc) when creating cavities in the PCM model, presumably H number 40 is not close enough to any other atom to form such a fragment, to overcome this place an explicit cavity on H number 40: In the SCRF input : SCRF=(PCM,Solvent=Chloroform,Read) Then after the coordinates: SPHEREONH=40 Hope this helps, keith --- "my-phuong pham phmphuong[a]yahoo.com" wrote: > > Sent to CCL by: "my-phuong pham" > [phmphuong.:.yahoo.com] > > From: my-phuong pham > phmphuong^^yahoo.com > > I have the optimized TS strcutre in gas phase and I > want to calculate SCF of it in solvent. Here are the > input and output and I don't satisfy with the error > notice in the output file: > UA0: Hydrogen 40 is unbound. Keep it explicit at > all point on the > UA0: potential energy surface to get meaningful > results. > > > %chk=e1P_ts_sol.chk > %mem=600mb > %nprocl=1 > %nprocs=2 > p b3lyp/6-31g(d,p) SCF=Tight > SCRF=(PCM,Solvent=Chloroform) Test nosym > > e1P_ts_sol > > 0 1 > C 0.00402900 -0.20828000 > -1.13297500 > C 0.16651600 1.13160700 > -1.76060400 > H -0.79808000 -0.28572500 > -0.41306000 > H 0.10681000 -1.03922100 > -1.81755800 > H 1.01177700 1.16692400 > -2.46789800 > O -1.07075800 0.93710500 > -2.35854000 > C 0.19555600 2.39892900 > -0.90625300 > H -0.02649100 3.22903100 > -1.59263800 > H -0.60180800 2.37803300 > -0.15101600 > O 1.46833400 2.60335800 > -0.28350800 > C 1.71515100 3.96299100 > 0.02591700 > H 2.70366700 4.02078600 > 0.48939500 > H 1.70956700 4.58783100 > -0.87896500 > H 0.96903500 4.36871100 > 0.72650300 > H -2.17804400 1.15158200 > -1.30274500 > C -3.67865300 0.24180200 > -0.39140700 > C -3.77166900 -0.76995500 > -1.36531600 > C -4.54532500 0.20561300 > 0.71490900 > C -4.71454300 -1.78730800 > -1.22384200 > H -3.10089200 -0.73894900 > -2.21834600 > C -5.48188900 -0.81803400 > 0.84160000 > H -4.47361200 0.99786500 > 1.45457900 > C -5.57468100 -1.82410300 > -0.12380500 > H -4.77679100 -2.56025400 > -1.98595000 > H -6.14811600 -0.82743900 > 1.70087800 > H -6.30754900 -2.61891400 > -0.02292300 > C 2.53621100 -1.11697100 > -0.32928600 > C 2.92297700 -2.45415300 > -0.48617400 > C 3.45309800 -0.08633000 > -0.57529400 > C 4.22692600 -2.75941500 > -0.87588900 > H 2.19265000 -3.23546300 > -0.29906800 > C 4.75486000 -0.40526900 > -0.96474300 > H 3.12497100 0.94394600 > -0.47975300 > C 5.14829200 -1.73710500 > -1.11367600 > H 4.52265300 -3.79792500 > -0.99556300 > H 5.46488400 0.39405600 > -1.15875200 > H 6.16235100 -1.97653700 > -1.41917200 > O -2.77747200 1.24399700 > -0.46969000 > O 1.24882200 -0.84546600 > 0.07207800 > H 1.07245500 -0.44149800 > 1.19919500 > N 0.79763000 -0.12051100 > 2.40464900 > C -0.66892900 0.09025900 > 2.49235900 > H -0.97672100 0.87863300 > 1.80359900 > H -1.18299100 -0.83067200 > 2.21051500 > H -0.95617500 0.36424100 > 3.51415500 > C 1.54494900 1.11784700 > 2.72429700 > H 2.61503700 0.90227900 > 2.69708000 > H 1.32565800 1.86357500 > 1.95902900 > H 1.27424900 1.48946700 > 3.71954400 > C 1.22383100 -1.25367900 > 3.25537700 > H 0.68342000 -2.15176400 > 2.95025400 > H 2.29384100 -1.42232500 > 3.11940700 > H 1.01917900 -1.04931600 > 4.31284100 > > > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > The output: > > Entering Gaussian System, Link 0=g03 > Input=e1P_ts_sol.com > Output=e1P_ts_sol.log > Initial command: > /uufs/arches/sys/g03/g03/l1.exe > /scratch/parallel/u0400086/180337.mmrm.privatearch.arches/Gau-2808.inp > -scrdir=/scratch/parallel/u0400086/180337.mmrm.privatearch.arches/ > Entering Link 1 = /uufs/arches/sys/g03/g03/l1.exe > PID= 2810. > > Copyright (c) > 1988,1990,1992,1993,1995,1998,2003,2004, Gaussian, > Inc. > All Rights Reserved. > > This is the Gaussian(R) 03 program. It is based on > the > the Gaussian(R) 98 system (copyright 1998, > Gaussian, Inc.), > the Gaussian(R) 94 system (copyright 1995, > Gaussian, Inc.), > the Gaussian 92(TM) system (copyright 1992, > Gaussian, Inc.), > the Gaussian 90(TM) system (copyright 1990, > Gaussian, Inc.), > the Gaussian 88(TM) system (copyright 1988, > Gaussian, Inc.), > the Gaussian 86(TM) system (copyright 1986, > Carnegie Mellon > University), and the Gaussian 82(TM) system > (copyright 1983, > Carnegie Mellon University). Gaussian is a > federally registered > trademark of Gaussian, Inc. > > This software contains proprietary and confidential > information, > including trade secrets, belonging to Gaussian, > Inc. > > This software is provided under written license and > may be > used, copied, transmitted, or stored only in accord > with that > written license. > > The following legend is applicable only to US > Government > contracts under FAR: > > RESTRICTED RIGHTS LEGEND > > Use, reproduction and disclosure by the US > Government is > subject to restrictions as set forth in > subparagraphs (a) > and (c) of the Commercial Computer Software - > Restricted > Rights clause in FAR 52.227-19. > > Gaussian, Inc. > 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 > > === message truncated === ___________________________________________________________ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html From owner-chemistry@ccl.net Tue Aug 28 19:31:01 2007 From: "Sina T reli sinatureli%x%gmail.com" To: CCL Subject: CCL: Placing RM1 parameters to PM3 Message-Id: <-35042-070828192125-1149-MnlCbBV028zsJo19gypwMA:_:server.ccl.net> X-Original-From: "Sina T reli" Date: Tue, 28 Aug 2007 19:21:22 -0400 Sent to CCL by: "Sina T reli" [sinatureli],[gmail.com] Greetings, I am working with biomolecules using spartan 04 and I would like to update my se methods to RM1 which has been shown to perform better for certain types of biomolecules (one is partially which I am working on). I have seen people replacing parameters in AM1 with those in RM1. But since the molecule I am working with contains MG, I need to use the PM3 method. I am wondering, will just replacing the paramters in PM3 with those in RM1 is likely to produce a good result? Because all the replacements I have seen is between AM1-RM1 Thanks, Sina