From wak@valera.anu.edu.au Fri Sep 27 01:58:03 1996 Received: from anugpo.anu.edu.au for wak@valera.anu.edu.au by www.ccl.net (8.7.5/950822.1) id BAA10791; Fri, 27 Sep 1996 01:27:35 -0400 (EDT) Received: from valera.anu.edu.au (valera.anu.edu.au [150.203.193.128]) by anugpo.anu.edu.au (8.7.6/8.6.12) with SMTP id PAA10043 for <@anugpo.anu.edu.au:chemistry@www.ccl.net>; Fri, 27 Sep 1996 15:27:35 +1000 (EST) Received: from localhost by valera.anu.edu.au via SMTP (950911.SGI.8.6.12.PATCH825/940406.SGI) for id PAA23316; Fri, 27 Sep 1996 15:27:34 +1000 Date: Fri, 27 Sep 1996 15:27:34 +1000 (EST) From: Bill King Reply-To: Bill.King@anu.edu.au To: chemistry@www.ccl.net Subject: Problem with Gaussian PM3 Mg parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I am having a problem with Gaussian94 PM3 calculations including Mg. As an example of this problem, please find below excerpts of an input and output that I used. It is not a problem of PM3, as Spartan's version of PM3 does not have this problem. Specifically, the distance between the Mg atom and the O atom of water seem ridiculously short. The complete input file for the calculation of water and a Mg atom: %Chk=sym #RHF/6-31G FOpt(MaxCycle=20) Geometrical optimization of Mg2+ and H2O 2 1 H O,1,R2 H,2,R3,1,A3 Mg,2,R4,1,A4,3,D4 Variables: R2=0.95 R3=0.94 R4=1.87340524 A3=110.2318868 A4=109.93587344 D4=-132.38580937 ---------------------------------- and after 20 optimization steps the output was: Optimization stopped. -- Number of steps exceeded, NStep= 20 -- Flag reset to prevent archiving. ---------------------------- ! Non-Optimized Parameters ! ! (Angstroms and Degrees) ! ------------------------ ------------------------- ! Name Definition Value Derivative Info. ! ----------------------------------------------------------------------------- ! R1 R(2,1) 3.5327 -DE/DX = 0.0163 ! ! R2 R(3,2) 3.5328 -DE/DX = 0.0163 ! ! R3 R(4,2) 0.4179 -DE/DX = 0.0639 ! ! A1 A(1,2,3) 99.5924 -DE/DX = 0.0106 ! ! A2 A(1,2,4) 49.9326 -DE/DX = 0.0053 ! ! A3 A(3,2,4) 49.8115 -DE/DX = 0.0053 ! ! D1 D(1,4,2,3) 185.4162 -DE/DX = 0.0001 ! ----------------------------------------------------------------------------- GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Note the units of distance here are Bohr radii!! Is there something wrong with the input file? Or is this a known problem? If I receive anything interesting I will summarize the replys. Thank you in advance for any help. Bill --- Bill King Division of Biochemistry and Molecular Biology email: Bill.King@anu.edu.au John Curtin School of Medical Research phone: +61-6-279-8302 PO Box 334 FAX: +61-6-249-5075 Canberra ACT 2601 Australia From daum@tec.fal.de Fri Sep 27 03:58:09 1996 Received: from hpcs11.dv.fal.de for daum@tec.fal.de by www.ccl.net (8.7.5/950822.1) id DAA12256; Fri, 27 Sep 1996 03:56:09 -0400 (EDT) Received: from Habicht.tec.fal.de by hpcs11.dv.fal.de with SMTP (1.38.193.4/16.2) id AA16511; Fri, 27 Sep 1996 09:56:01 +0200 Message-Id: <324C0720.1117@tec.fal.de> Date: Fri, 27 Sep 1996 09:56:00 -0700 From: Joerg Daum Organization: FAL Braunschweig, Germany X-Mailer: Mozilla 2.02 (Win16; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: request-molecular modelling in heterogenous catalysis X-Url: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Institut f. Technische Chemie / Institute of Technical Chemistry to whom it may concern We are concerned with applied heterogeneous catalysis, e.g. nitrate removal from drinking water (three-phase system), and are interestet in models of the catalytic process. Does anybody knows wether software exists (for non-specialists), which allows to model metal surfaces (e.g. Pd) and reactions of small inorganic molecules (e.g. nitrate, nitrite, hydrogen) on these surfaces ? Thank you very much for your support. Jörg Daum (Doktorand / Ph.D. student) daum@tec.fal.de Technische Universität Braunschweig Hans-Sommer-Strasse 10, D-38106 Braunschweig, Germany From wak@valera.anu.edu.au Fri Sep 27 04:05:41 1996 Received: from anugpo.anu.edu.au for wak@valera.anu.edu.au by www.ccl.net (8.7.5/950822.1) id DAA12216; Fri, 27 Sep 1996 03:47:27 -0400 (EDT) Received: from valera.anu.edu.au (valera.anu.edu.au [150.203.193.128]) by anugpo.anu.edu.au (8.7.6/8.6.12) with SMTP id RAA25628 for <@anugpo.anu.edu.au:chemistry@www.ccl.net>; Fri, 27 Sep 1996 17:47:26 +1000 (EST) Received: from localhost by valera.anu.edu.au via SMTP (950911.SGI.8.6.12.PATCH825/940406.SGI) for id RAA24373; Fri, 27 Sep 1996 17:47:25 +1000 Date: Fri, 27 Sep 1996 17:47:25 +1000 (EST) From: Bill King Reply-To: Bill.King@anu.edu.au To: chemistry@www.ccl.net Subject: CORRECTION Problem with Gaussian PM3 Mg parameters. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry, The input file in my previous message wa in correct! I have made the correction below. I have replaced "RHF/6-31G" with PM3 Sorry for the goof... Here is the corrected message. Dear netters, I am having a problem with Gaussian94 PM3 calculations including Mg. As an example of this problem, please find below excerpts of an input and output that I used. It is not a problem of PM3, as Spartan's version of PM3 does not have this problem. Specifically, the distance between the Mg atom and the O atom of water seem ridiculously short. The complete input file for the calculation of water and a Mg atom: %Chk=sym #PM3 FOpt(MaxCycle=20) Geometrical optimization of Mg2+ and H2O 2 1 H O,1,R2 H,2,R3,1,A3 Mg,2,R4,1,A4,3,D4 Variables: R2=0.95 R3=0.94 R4=1.87340524 A3=110.2318868 A4=109.93587344 D4=-132.38580937 ---------------------------------- and after 20 optimization steps the output was: Optimization stopped. -- Number of steps exceeded, NStep= 20 -- Flag reset to prevent archiving. ---------------------------- ! Non-Optimized Parameters ! ! (Angstroms and Degrees) ! ------------------------ ------------------------- ! Name Definition Value Derivative Info. ! ----------------------------------------------------------------------------- ! R1 R(2,1) 3.5327 -DE/DX = 0.0163 ! ! R2 R(3,2) 3.5328 -DE/DX = 0.0163 ! ! R3 R(4,2) 0.4179 -DE/DX = 0.0639 ! ! A1 A(1,2,3) 99.5924 -DE/DX = 0.0106 ! ! A2 A(1,2,4) 49.9326 -DE/DX = 0.0053 ! ! A3 A(3,2,4) 49.8115 -DE/DX = 0.0053 ! ! D1 D(1,4,2,3) 185.4162 -DE/DX = 0.0001 ! ----------------------------------------------------------------------------- GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Note the units of distance here are Bohr radii!! Is there something wrong with the input file? Or is this a known problem? If I receive anything interesting I will summarize the replys. Thank you in advance for any help. Bill --- Bill King Division of Biochemistry and Molecular Biology email: Bill.King@anu.edu.au John Curtin School of Medical Research phone: +61-6-279-8302 PO Box 334 FAX: +61-6-249-5075 Canberra ACT 2601 Australia From Gerhard.Bischof@uibk.ac.at Fri Sep 27 08:58:15 1996 Received: from uibk.ac.at for Gerhard.Bischof@uibk.ac.at by www.ccl.net (8.7.5/950822.1) id IAA13349; Fri, 27 Sep 1996 08:25:13 -0400 (EDT) Received: from s06subz2.uibk.ac.at by uibk.ac.at with SMTP id AA29906 (5.65c/IDA-1.4.4 from c72463@s06subz2.uibk.ac.at for ); Fri, 27 Sep 1996 14:25:02 +0200 Received: from S06SUBZ2/SpoolDir by s06subz2.uibk.ac.at (Mercury 1.21); 27 Sep 96 14:25:12 +0100 Received: from SpoolDir by S06SUBZ2 (Mercury 1.30); 27 Sep 96 14:25:07 +0100 From: "GERHARD BISCHOF" Organization: University of Innsbruck, Austria To: chemistry@www.ccl.net Date: Fri, 27 Sep 1996 14:24:48 +0100 Subject: quaternions X-Confirm-Reading-To: "GERHARD BISCHOF" X-Pmrqc: 1 Priority: normal X-Mailer: Pegasus Mail for Windows (v2.23) Message-Id: <3EA2C295532@s06subz2.uibk.ac.at> hello all i am using the leapfrog\quaternion algorithm from Allen&Tildesley to simulate the dynamics of cations in water. with the timestep of 0.3 fs i observe a strong increase in energy after about 300 timesteps and the waters fly away from the ion. doing the same simulation without keeping the waters rigid works well. has anybody else had a similar experience ? thanks for any help, gerhard ************************************************************************** Gerhard Bischof E-mail:Gerhard.Bischof@uibk.ac.at Tel:<0043>512-507-5154 Fax:<0043>512-507-2934 Universitaet Innsbruck Inst. f. Allg., Anorg. und Theor. Chemie Innrain 52 A-6020 Innsbruck Austria *************************************************************************** From wchipman@bridgew.edu Fri Sep 27 09:58:10 1996 Received: from topcat.bridgew.edu for wchipman@bridgew.edu by www.ccl.net (8.7.5/950822.1) id JAA13762; Fri, 27 Sep 1996 09:49:54 -0400 (EDT) Received: by topcat.bridgew.edu (MX V4.2 AXP) id 71; Fri, 27 Sep 1996 09:49:13 EST5EDT4,M4.1.0,M10.5.0 Sender: wchipman@bridgew.edu Date: Fri, 27 Sep 1996 09:49:13 EST5EDT4,M4.1.0,M10.5.0 From: wchipman@topcat.bridgew.edu Reply-To: wchipman@bridgew.edu To: CHEMISTRY@www.ccl.net Message-ID: <009A8FE1.9A3A8382.71@topcat.bridgew.edu> Subject: lysozyme:NAM-NAG-NAM pdb file? Hi, Can anyone give me the PDB identifier (or other location) of an X-Ray crystallographic file for the NAM-NAG-NAM:lysozyme complex, or give me any information that would point me at such a file, or a similar one? I have PDB1hew.ent and a number of lysozyme structures. I would like this for a computer aided instructional module in biochemistry. Thanks very much. Bill Chipman wchipman@bridgew.edu Bridgewater State College Bridgewater, MA 02325 From chipman@bridgew.edu Fri Sep 27 10:58:23 1996 Received: from topcat.bridgew.edu for chipman@bridgew.edu by www.ccl.net (8.7.5/950822.1) id KAA13983; Fri, 27 Sep 1996 10:23:54 -0400 (EDT) Received: by topcat.bridgew.edu (MX V4.2 AXP) id 272; Fri, 27 Sep 1996 10:23:48 EST5EDT4,M4.1.0,M10.5.0 Sender: chipman@bridgew.edu Date: Fri, 27 Sep 1996 10:23:48 EST5EDT4,M4.1.0,M10.5.0 From: chipman@topcat.bridgew.edu Reply-To: chipman@bridgew.edu To: CHEMISTRY@www.ccl.net Message-ID: <009A8FE6.6F001FE7.272@topcat.bridgew.edu> Subject: lysozyme:NAM-NAG-NAM structure file? Hi, Can anyone give me a PDB identifier or otherwise point me at an X-ray (or other) file for the NAM-NAG-NAM complex with lysozyme? I have PDB1HEW.ENT and a bunch of lysozyme PDB files. I would like the file for some CAI I am doing in biochemistry. Thanks in advance. Bill Chipman wchipman@bridgew.edu From pran@osuunx.ucc.okstate.edu Fri Sep 27 11:03:10 1996 Received: from osuunx.ucc.okstate.edu for pran@osuunx.ucc.okstate.edu by www.ccl.net (8.7.5/950822.1) id KAA14139; Fri, 27 Sep 1996 10:47:42 -0400 (EDT) Date: Fri, 27 Sep 1996 09:45:11 -0500 (CDT) From: Ran Pan To: chemistry@www.ccl.net cc: pran@osuunx.ucc.okstate.edu Subject: Help with AM1 (or MOPAC) In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: pran@osuunx.ucc.okstate.edu Dear neter, I am trying to work on some compounds containing transition metals by using mopac. However, I found that this package do not contain the defined parameters for transition metal atom. Could some experts in mopac give me some tips on how to treat this kind of systems. I appreciate your help very much. Sincerely, Ran Pan From val@nmr1.ioc.ac.ru Fri Sep 27 11:58:14 1996 Received: from nmr1.ioc.ac.ru for val@nmr1.ioc.ac.ru by www.ccl.net (8.7.5/950822.1) id LAA14930; Fri, 27 Sep 1996 11:52:51 -0400 (EDT) Received: from [193.233.3.193] (nmr2.ioc.ac.ru [193.233.3.193]) by nmr1.ioc.ac.ru (8.6.12/8.6.9) with SMTP id TAA01214 for ; Fri, 27 Sep 1996 19:53:34 +0400 Date: Fri, 27 Sep 96 19:53:31 +0300 From: "Ananikov V.P." Message-Id: <81861.val@nmr1.ioc.ac.ru> X-Minuet-Version: Minuet1.0_Beta_17A Reply-To: X-POPMail-Charset: IBM 8-Bit To: chemistry@www.ccl.net Subject: MOL to HPGL convertion Dear CCl's, I want to write my own converter from MOL to HPGL format which can work as a pipe. and I need your help: Does anyone can help me to find a full description of MOL format? Does anyone know where can I find the sources of such programs (for any platforms, DOS, WINDOWS, UNIX, etc.)? Please write direct to me, I will summarize. thank you. sincerely, Ananikov V. From EDWARDSP@edinboro.edu Fri Sep 27 12:10:20 1996 Received: from hydra.vax.edinboro.edu for EDWARDSP@edinboro.edu by www.ccl.net (8.7.5/950822.1) id LAA14677; Fri, 27 Sep 1996 11:28:06 -0400 (EDT) Received: from edinboro.edu by edinboro.edu (PMDF V4.3-10 #2652) id <01I9YZQLF7EO90N0T2@edinboro.edu>; Fri, 27 Sep 1996 11:28:09 -0500 (EST) Date: Fri, 27 Sep 1996 11:28:09 -0500 (EST) From: "Dr. Paul Edwards" Subject: CCL: SIBIQ To: chemistry@www.ccl.net Message-id: <01I9YZQLG9ZM90N0T2@edinboro.edu> X-VMS-To: IN%"chemistry@www.ccl.net" X-VMS-Cc: EDWARDSP MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I'm trying to find a program for doing Semi-Empirical Molecular Orbital calculations called SIBIQ. I've done Yahoo and Lycos searches and all the leads point toward an FTP address which no longer exists. Does anyone know where it can be found or have a copy they'd be willing to share? Thanks! Paul Edwards Associate Professor of Chemistry Edinboro University of PA edwardsp@edinboro.edu From rochus@felix.anorg.chemie.tu-muenchen.de Fri Sep 27 12:58:14 1996 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.7.5/950822.1) id MAA15404; Fri, 27 Sep 1996 12:56:59 -0400 (EDT) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) id RAA28233; Fri, 27 Sep 1996 17:56:52 +0100 From: "Rochus Schmid" Message-Id: <9609271756.ZM28231@felix> Date: Fri, 27 Sep 1996 17:56:51 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: f77 comp. on DEC alpha Cc: rochus@felix.anorg.chemie.tu-muenchen.de, wolfgang@felix.anorg.chemie.tu-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters, We currently have some problems to compile a DFT-programm (deMon 1.1) on our new DEC Alpha. We didn't have any trouble to compile it and get it running on our SGI (R4400). It works and produces correct values. However, we don't have a lot of experience with Alphas. So after solving some minor compiling and linking problems we have an executable now. After reading the input it stops while building the grids with the error message: unaligned access ..... I have the feeling (however, I'm possibly completely wrong, pleas e forgive me in that case ;-) that the problem of the 64 bit architecture and the code is not "suited" to that, since the same thing is running fine on the SGI. Can anyone of you give us a hint: - did anyone build deMon on an Alpha? - is this a common problem when porting to Alphas (maybe this is not specific to our code)? - what kind of constructions can be the origin of the problem? Is there something specific to check in the code? Any help is very much appreciated. Thank you very much. Best greetings from Munich, Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 2891 3140 Lehrstuhl f. Anorganische Chemie 1 Fax. ++49 89 2891 3088 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From ren@chvzmw.chem.ncsu.edu Fri Sep 27 14:58:15 1996 Received: from chvzmw for ren@chvzmw.chem.ncsu.edu by www.ccl.net (8.7.5/950822.1) id OAA15927; Fri, 27 Sep 1996 14:39:21 -0400 (EDT) From: Date: Fri, 27 Sep 1996 14:37:19 -0400 Message-Id: <96092714371971@chvzmw.chem.ncsu.edu> To: CHEMISTRY@www.ccl.net Subject: Help! Chemical shift of water? X-VMS-To: CHEMISTRY@www.ccl.net Hi, Friends: I am looking for the theoretical studies on the chemical shift of water. I will appreciate it if anybody can inform me of the current publications. Thank you in advance. J. Ren REN@CHVZMW.CHEM.NCSU.EDU