From h8714031@hkuxa.hku.hk Thu Oct 21 04:09:42 1993 From: h8714031@hkuxa.hku.hk (Mok Kam Wah) Message-Id: <9310210717.AA25479@hkuxb.hku.hk> Subject: Question on calculating vibrational frequency To: chemistry@ccl.net (Computational Chemistry) Date: Thu, 21 Oct 93 15:17:45 WST Dear Netters, I am doing ab initio calculation on diatomics. I want to ask is it justified to calculate vibrational frequency in the following way. First to optimized to the equilibrium geometry. Calculate the energy (say 0.01A) apart from the geometry. Thus the potentail well mininium and a nearby point can then determine the quadratic curve pass thru them. Use 2 times the coeff of x**2 as the force constant and vibrational frequency = sqrt (force constant / isotopic mass) Is the accuracy of this calculation similiar to the vibrational analysis available in most Ab initio package? K.W.Mok -- K.W.Mok E-Mail: h8714031@hkuxa.hku.hk Dept. of Chem., University of Hong Kong. From h.rzepa@ic.ac.uk Thu Oct 21 08:39:04 1993 Message-Id: <9310210840.AA07126@cscmgb.cc.ic.ac.uk> Date: Thu, 21 Oct 1993 08:39:04 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: American Chemical Society gopher (fwd) Excellent idea. Might I take it further by suggesting the gopher might carry information NOT on the ACS pages! For example, color plates, which are currently very expensive, might be archived here. Further, animations can also be added. Just in case you have not noticed, we have been running our own gopher for this purpose for a year or more. It contains animations, sound, colour plates, programs etc etc. It can be accessed as argon-fddi.ch.ic.ac.uk (155.198.1.33). Clearly the problem confronting us is how to ensure quality of this material. Gopher is a highly distributed concept. Do we want to have say only one ACS and one RSC gopher, which is tightly controlled by the societies? This would ensure security, quality control, peer review mechanisms etc. But is it within the gopher concept of a distributed system? Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.4, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From tolja@maya.geo.uu.se Thu Oct 21 13:49:17 1993 Date: Thu, 21 Oct 93 12:49:17 +0100 From: tolja@maya.geo.uu.se (Anatoli Belonoshko) Message-Id: <9310211149.AA04038@maya.geo.uu.se.geo> To: chemistry@ccl.net Subject: Coordinate file format transformation Dear communitists, I need to transform XYZ (best of all) or other formats of file containing atomic coordinates into PDB format. If anyone aware about such public domain or easily available programs, could you please let me know. Thank you. Anatoly Belonoshko Uppsala University, Sweden e-mail: tolja@maya.geo.uu.se From raman@bioc01.uthscsa.edu Thu Oct 21 04:36:13 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9310211436.AA08900@bioc01.uthscsa.edu> Subject: RASMOL 2.2 To: chemistry@ccl.net Date: Thu, 21 Oct 1993 09:36:13 -0500 (CDT) Dear Netters RASMOL 2.2 can be FTPed from ftp.dcs.ed.ac.uk (129.215.160.5) and can be found in the directory /pub/rasmol. Its features are quite good! Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From raman@bioc01.uthscsa.edu Thu Oct 21 04:39:24 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9310211439.AA08909@bioc01.uthscsa.edu> Subject: Re:RASMOL 2.2. To: chemistry@ccl.net Date: Thu, 21 Oct 1993 09:39:24 -0500 (CDT) Dear Netters I forgot to mention in my previous posting that there is also a WINDOWS version of RASMOL at the same FTP site. I will be happy to provide further details if anyone is interested. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From young@slater.cem.msu.edu Thu Oct 21 07:07:37 1993 Date: Thu, 21 Oct 93 11:07:37 -0400 From: young@slater.cem.msu.edu (Dave Young) Message-Id: <9310211507.AA21025@slater.cem.msu.edu> To: chemistry@ccl.net Subject: vibrational calculation There was a question about getting vibrational frequencies by calculating points near the equilibrium geometry. The answer is that you need at least three point to do a least squares fit to a quadratic, and this will work. However, it is better to do more points (5-7) and then a least squares fit to a morse potential or a higher order polynomial. If you're not sure how to get the frequency from this, check the book "Molecular Vibrations" by Wilson, Decius and Cross. Dave Young young@slater.cem.msu.edu youngdc@msucem From JFO555F%SMSVMA.BITNET@phem3.acs.ohio-state.edu Thu Oct 21 09:23:50 1993 Date: Thu, 21 Oct 1993 14:23:50 -0500 (CDT) From: Jim O'Brien Subject: gaussian 92 on S2 To: chemistry@ccl.net Message-Id: <01H4DPUT4C3M8X41G4@phem3.acs.ohio-state.edu> I am trying to run gaussian 92 on the S2 molecule. I keep getting an error in Lnkle. I have tried guess=huckel and guess=core. I have tried rhf and uhf. Any help will be appreciated. Jim O'Brien From mercie@med.cornell.edu Thu Oct 21 13:03:54 1993 Date: Thu, 21 Oct 1993 17:03:54 -0400 (EDT) From: Gustavo Mercier Subject: brownian dynamics To: chemistry@ccl.net Message-Id: hi netters! With the goal of performing brownian dynamics to explore the interaction of water with a modest size metalloporphyrin, I would like to identify the available programs in this area. I understand that the MD extension to X-Plor and Charmm have this capability and MOTECC-93(?) KGNMD can do the same. Are there any others? Please send answers to me and I will summarize for the net. thanks gus mercier mercie@cumc.cornell.edu From HARMON@wmich.edu Thu Oct 21 14:13:10 1993 Date: Thu, 21 Oct 1993 18:13:10 -0400 (EDT) From: HARMON@wmich.edu Subject: EQUIPMENT NEEDED TO MAKE SLIDES FROM COMPUTER GRAPHICS To: CHEMISTRY@ccl.net Message-Id: <01H4DTIFBJUQ94PMXY@wmich.edu> To Netters: Could anyone furnish me with some information on manufacturers or suppliers of equipment which one can attach to one's computer in order to convert Powerpoint or other slide maker software graphics to slides containing chemical structures and other information. At present we are using Chemwindows to draw our structures which we then save under a WPG format and take them over to our Media Services where they then put them in Microsoft's Powerpoint on a Mac and make the slides. Is there a better program out there than Powerpoint for making slides. Any information would be deeply appreciated. Bob Harmon Professor of Chemistry Department of Chemistry Western Michigan University Kalamazoo, Mi 49008-3842 Phone (616)387-2945 Fax (616)387-2943 Internet: "Robert.Harmon@wmich.edu" From schurko@CC.UManitoba.CA Thu Oct 21 12:31:44 1993 Date: Thu, 21 Oct 1993 17:31:44 -0500 (CDT) From: Robert Schurko Subject: GAUSSIAN 92 query To: chemistry@ccl.net Message-Id: Does anyone know of a setting in G-92 which allows one to have the integral values (i.e. exchange, coulomb, overlap) printed within the output file? (It's a small molecule, don't worry.). Thanks a lot, Rob ============================================================================= schurko@ccu.umanitoba.ca Robert Schurko Chemistry Department (204)-474-9335 University of Manitoba Winnipeg, MB, CANADA ============================================================================= From Y0XIAO01@ULKYVX.LOUISVILLE.EDU Thu Oct 21 15:28:57 1993 Date: Thu, 21 Oct 1993 20:28:57 -0500 (EST) From: "Leon Y. Xiao, (502)635-6931" Subject: RASMOL 2.2 To: chemistry@ccl.net Message-Id: <01H4DY5Q030M8WXYUO@ULKYVX.LOUISVILLE.EDU> Hi, netters: I have downloaded the RASMOL MS Window version and tested it. It is a nice graphic viewing tool ! You only need one file: RASWIN.exe. Leon Xiao University of Louisville