From mw@crystal.uwa.edu.au Thu Dec 19 01:10:35 1996 Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by www.ccl.net (8.8.3/950822.1) id AAA28916; Thu, 19 Dec 1996 00:16:19 -0500 (EST) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.8.3/8.8.0) with SMTP id NAA24958 for ; Thu, 19 Dec 1996 13:16:14 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA04660; Thu, 19 Dec 1996 15:39:28 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9612190516.AA01796@pack.crystal.uwa.edu.au> Subject: Ca(H2PO4)2.H2O? To: CHEMISTRY@www.ccl.net Date: Thu, 19 Dec 96 13:16:09 WST Mailer: Elm [revision: 70.85] Hello, Does any one know the space group of Ca(H2PO4)2.H2O, it was not reported in the Neutron Diffraction Study paper and I can't get hold of earier X-ray paper. Or maybe how could I find it. Thank you. magda (mw@crystal.uwa.edu.au) From kolar@surf.pangea.ca Thu Dec 19 02:10:35 1996 Received: from surf.pangea.ca for kolar@surf.pangea.ca by www.ccl.net (8.8.3/950822.1) id BAA29183; Thu, 19 Dec 1996 01:50:38 -0500 (EST) Received: from localhost (kolar@localhost) by surf.pangea.ca (8.7.6/8.7.3) with SMTP id AAA01448 for ; Thu, 19 Dec 1996 00:49:12 -0600 (CST) Date: Thu, 19 Dec 1996 00:49:12 -0600 (CST) From: Miroslav Kolar To: chemistry@www.ccl.net Subject: Reaction-diffusion solver, C Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Would you like to try TRANSIENT - a new reaction-diffusion equations solver? For more details, visit: http://www.pangea.ca/~kolar/trans.htm HERE IS AT LEAST A SHORT DESCRIPTION: TRANSIENT is a C program for the time-dependent solution of arbitrary systems of generally nonlinear, parabolic partial differential equations in two variables (space and time), in particular, reaction-diffusion equations. An efficient adaptable time-stepping algorithm is applied. User has to supply a problem definition module (PDM) for each system of equations. A detailed 39 page manual, and demonstration PDM's for four different problems are supplied with the package. One of the demonstration PDM's deals with the simulation of the uniform corrosion of a metal surface and the diffusion of the corrosion products into two consecutive adjacent porous media. This module uses a nonequidistant spatial grid in order to treat adequately (with an increased precision) the important region near the corroding surface. The second demonstration PDM treats in a simplified way a gas generation in a closed space and its diffusion out through a narrow pipe. The third deals with an idealized model of stochastic surface growth, and the fourth with the Brusselator model of the mathematical biology. Mirek Kolar kolar@pangea.ca http://www.pangea.ca/~kolar/ From ps@ocisgi7.unizh.ch Thu Dec 19 04:10:41 1996 Received: from rzusuntk.unizh.ch for ps@ocisgi7.unizh.ch by www.ccl.net (8.8.3/950822.1) id DAA29632; Thu, 19 Dec 1996 03:17:47 -0500 (EST) Received: from ocisgi7.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.14) id AA22326; Thu, 19 Dec 96 09:17:44 +0100 Received: by ocisgi7.unizh.ch (950215.SGI.8.6.10/920502.SGI) id JAA04210; Thu, 19 Dec 1996 09:17:43 +0100 From: ps@ocisgi7.unizh.ch (Serge Pachkovsky) Message-Id: <199612190817.JAA04210@ocisgi7.unizh.ch> Subject: Re: CCL:G:spherical -> cartesian gaussians To: jim@gnosis.chem.queensu.ca (Jim Clark) Date: Thu, 19 Dec 1996 09:17:43 +0100 (MET) Cc: chemistry@www.ccl.net In-Reply-To: from "Jim Clark" at Dec 18, 96 07:14:16 pm X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > I have a wavefunction written in terms of spherical gaussian primitives > and I would like to rewrite it in terms of cartesian gaussians. As you > would expect, I'm having no problem with s-type and p-type primitives but > I'm already having trouble keeping the wavefunction normalized when using > a d-shell of primitives. H.B. Schlegel, M.J. Frisch, "Transformation Between Cartesian and Pure Spherical Harmonic Gaussians", Int. J. Quantum. Chem., vol. 54, pp. 83-87 (1995). Regards, /Serge.P From ypwitkow@cyf-kr.edu.pl Thu Dec 19 04:28:16 1996 Received: from info.cyf-kr.edu.pl for ypwitkow@cyf-kr.edu.pl by www.ccl.net (8.8.3/950822.1) id DAA29683; Thu, 19 Dec 1996 03:46:06 -0500 (EST) Received: from kinga.cyf-kr.edu.pl (5294@kinga.cyf-kr.edu.pl [149.156.4.10]) by info.cyf-kr.edu.pl (8.8.4/8.8.4) with ESMTP id JAA12041 for ; Thu, 19 Dec 1996 09:46:00 +0100 (MET) Received: (from ypwitkow@localhost) by kinga.cyf-kr.edu.pl (8.8.4/8.8.4) id JAA17285; Thu, 19 Dec 1996 09:45:51 +0100 (MET) From: Lucyna Kunert-Witkowska Message-Id: <199612190845.JAA17285@kinga.cyf-kr.edu.pl> Subject: Summary: MOPAC 93 on HP or SGI To: chemistry@www.ccl.net Date: Thu, 19 Dec 1996 09:45:50 +0100 (MET) Cc: ypwitkow@kinga.cyf-kr.edu.pl (Lucyna Kunert-Witkowska) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Dear all, Yesterday I posted a question about availibility of MOPAC 93 on HP or SGI platforms. Thank you VERY MUCH for all answers. Especially: James J. P. Stewart Park, TAE-YUN George P. Ford Dr. Satyam Priyadarshy Chris Borrill (thank you for Makefile!) Peter Blandon Dr. Jose Santiago Duca Rainer Koch Georg Ostertag I can summarize that this version of MOPAC 93 is truly portable and is running successfully on HP, SGI ONYX (IRIX 6.1), IBM (AIX 4.1) and DEC Alpha platforms. The only modification is needed in Makefile and in date and time functions. Compilation for SGI needs -static option. Thank you again and wish you all VERY HAPPY NEW YEAR! Lucyna Witkowska -- /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Lucyna Witkowska Academic Computer Centre ypwitkow@cyf-kr.edu.pl CYFRONET-Krakow, http://www.cyf-kr.edu.pl/~ypwitkow/ Nawojki 11,30-950 Krakow,Poland From gertvh@sci.kun.nl Thu Dec 19 06:10:38 1996 Received: from wn1.sci.kun.nl for gertvh@sci.kun.nl by www.ccl.net (8.8.3/950822.1) id GAA00217; Thu, 19 Dec 1996 06:06:08 -0500 (EST) Received: from mlfsilly.sci.kun.nl by wn1.sci.kun.nl via mlfsilly.sci.kun.nl [131.174.81.1] with SMTP for <@wn1.sci.kun.nl:CHEMISTRY@www.ccl.net> id MAA09129 (8.8.4/3.12); Thu, 19 Dec 1996 12:05:57 +0100 (MET) Received: by mlfsilly.sci.kun.nl (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id MAA17927; Thu, 19 Dec 1996 12:12:48 +0100 From: "Gert von Helden" Message-Id: <9612191212.ZM17925@mlfsilly.sci.kun.nl> Date: Thu, 19 Dec 1996 12:12:46 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Bond length in solid and gas phase Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everybody, I would be interested if there is a 'rule of thumb' about differences in bond length (and angles) between solid and gase phase organic molecules. Specifically, we are interested in diphenylamine and would like to know if one can use the solid state (x-ray) data and somehow scale it to a gas phase value. Thanks, Gert -- Gert von Helden Dept. of molecular and Laser Physics, University of Nijmegen, Netherlands e-mail: gertvh@sci.kun.nl, phone: (+31) 24 3652179, fax: (+31) 24 3653311 From peon@medchem.dfh.dk Thu Dec 19 08:10:41 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id IAA01863; Thu, 19 Dec 1996 08:03:06 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id OAA23626; Thu, 19 Dec 1996 14:03:02 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA11025; Thu, 19 Dec 1996 14:26:44 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Dec 1996 14:03:02 +0100 To: "Gert von Helden" From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:Bond length in solid and gas phase Cc: CHEMISTRY@www.ccl.net Hi Gert, >I would be interested if there is a 'rule of thumb' about differences >in bond length (and angles) between solid and gase phase organic >molecules. We can actually do better than a rule of thumb. MM3 (that is, Allingers original MM3, none of the copies, this is the Mac version) can calculate the difference between bond lengths from different determination methods, at least the part that is due to centrifugal distortion and anharmonic vibration. I guess this is sufficient? It still gives nuclear distances, so it's not appropriate for X-ray hydrogens for example, but the difference between electron density center and nuclear position shouldn't be significant for heavy atoms in the X-ray (I'm not entirely sure how much the nitrogen lone pair will affect the position in the X-ray though). >Specifically, we are interested in diphenylamine and would >like to know if one can use the solid state (x-ray) data and somehow >scale it to a gas phase value. One problem here, the usual with MM3. We don't have all parameters. However, using an "amide" (sp2) nitrogen and guessing a single parameter, I calculated the following table for diphenyl amine: VIBRATIONAL AMPLITUDE AND CENTRIFUGAL DISTORTION CONTRIBUTION TO THE BOND LENGTH BOND R(g) R(z) R(alp) R(e) R(a) 2( C)- 1( C) 1.3966 1.3926 1.3849 1.3888 1.3951 3( C)- 2( C) 1.3975 1.3936 1.3825 1.3897 1.3960 4( C)- 3( C) 1.4009 1.3963 1.3786 1.3930 1.3994 5( C)- 4( C) 1.3966 1.3926 1.3849 1.3888 1.3951 6( C)- 1( C) 1.3959 1.3909 1.3731 1.3881 1.3944 6( C)- 5( C) 1.3960 1.3913 1.3781 1.3883 1.3946 7( H)- 1( C) 1.1032 1.0855 1.0749 1.0805 1.0978 8( H)- 2( C) 1.1008 1.0837 1.0711 1.0783 1.0954 9( H)- 4( C) 1.1029 1.0859 1.0753 1.0802 1.0975 10( H)- 5( C) 1.1033 1.0852 1.0701 1.0805 1.0979 11( H)- 6( C) 1.1032 1.0857 1.0787 1.0805 1.0978 12( N)- 3( C) 1.4247 1.4210 1.4156 1.4167 1.4232 13( H)- 12( N) 1.0274 1.0106 1.0096 1.0078 1.0224 14( C)- 12( N) 1.4247 1.4210 1.4156 1.4167 1.4232 15( C)- 14( C) 1.3974 1.3934 1.3823 1.3896 1.3959 16( C)- 15( C) 1.3967 1.3927 1.3850 1.3889 1.3952 17( C)- 16( C) 1.3958 1.3908 1.3730 1.3880 1.3943 18( C)- 17( C) 1.3961 1.3914 1.3782 1.3884 1.3947 19( C)- 14( C) 1.4010 1.3964 1.3787 1.3932 1.3995 19( C)- 18( C) 1.3965 1.3925 1.3848 1.3887 1.3950 20( H)- 15( C) 1.1008 1.0837 1.0711 1.0783 1.0954 21( H)- 16( C) 1.1032 1.0855 1.0749 1.0805 1.0978 22( H)- 17( C) 1.1032 1.0857 1.0787 1.0805 1.0978 23( H)- 18( C) 1.1033 1.0852 1.0701 1.0805 1.0979 24( H)- 19( C) 1.1029 1.0859 1.0753 1.0802 1.0975 The two first columns are gas phase values (expected from electron diffraction and microwave), then comes expected X-ray values (thermal averages of nuclear positions at 298 K), minimum energy nuclear positions (appropriate for ab initio), and one more value I don't know exactly, but I guess it's gas phase also (thermal average of distance with r-1 weighting). Take your pick. Even though absolute values may be off (one guessed parameter, remember), relative ones should be OK. Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From raeker@saturn.kent.edu Thu Dec 19 11:10:41 1996 Received: from saturn.kent.edu for raeker@saturn.kent.edu by www.ccl.net (8.8.3/950822.1) id KAA02527; Thu, 19 Dec 1996 10:17:13 -0500 (EST) Received: by saturn.kent.edu (AIX 4.1/UCB 5.64/4.03) id AA18220; Thu, 19 Dec 1996 10:04:35 -0500 Date: Thu, 19 Dec 1996 10:04:35 -0500 (EST) From: "Todd J. Raeker" To: CCL Subject: CCL: Need OpenGL code for Molecule Display Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Graphics Programmers, Does anyone have sample OpenGL code for 3D display of molecules (stick, ball and stick, or CPK) that they would be willing to share. I am working on a GUI for some of my programs and would like to include display of molecules and density surfaces. I can do the coding myself but it would take some of my very precious time I have little to spare these days. Thanks for any help. Regards. Todd. Dr. Todd J. Raeker Department of Chemistry Theoretical Chemistry Group Kent State University raeker@saturn.kent.edu Kent, OH 44242-0001 http://www.saturn.kent.edu/Raeker Phone (216)-672-2986 From yun.tang@csb.ki.se Thu Dec 19 13:10:44 1996 Received: from e45.it.ki.se for yun.tang@csb.ki.se by www.ccl.net (8.8.3/950822.1) id MAA04440; Thu, 19 Dec 1996 12:32:18 -0500 (EST) Received: from thon.csb.ki.se (thon.csb.ki.se [130.237.204.199]) by e45.it.ki.se (8.7.5/8.7.3) with SMTP id SAA20762 for ; Thu, 19 Dec 1996 18:30:10 +0100 (MET) Received: from pike.csb.ki.se by thon.csb.ki.se (4.1/SMI-4.1) id AA15750; Thu, 19 Dec 96 18:35:25 +0100 Received: from sill.csb.ki.se by pike.csb.ki.se; (5.65/1.1.8.2/03May94-0316PM) id AA06991; Thu, 19 Dec 1996 18:32:10 +0100 Message-Id: <32B97BFF.2BB0@csb.ki.se> Date: Thu, 19 Dec 1996 18:31:43 +0100 From: Yun Tang Reply-To: yun.tang@csb.ki.se Organization: Karolinska Institute X-Mailer: Mozilla 3.0 (Win95; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: How to perform MD on unstable protein? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, When I performed molecular dynamics on a protein within a water sphere using CHARMM program, the protein relaxed and became loose after 10ps. The protein structure was extracted from a complex determined by NMR. Then I performed MD on the complex, the protein also relaxed. Maybe the protein is unstable. So my question is how to handle unstable protein in order to perform MD. Any help that you could give me will be appreciated! Thanks in advance! Season's greetings and best wishes to all! Dr. Yun Tang Karolinska Institute email: yun.tang@csb.ki.se