From Xiaoming.Zheng@unsw.EDU.AU Wed Feb 7 00:11:01 1996 Received: from sam.comms.unsw.EDU.AU for Xiaoming.Zheng@unsw.EDU.AU by www.ccl.net (8.6.10/950822.1) id XAA12856; Tue, 6 Feb 1996 23:57:00 -0500 Received: from smtp.unsw.edu.au ([149.171.76.148]) by sam.comms.unsw.EDU.AU (8.6.9/8.6.9.kenso-central) with SMTP id PAA20417 for ; Wed, 7 Feb 1996 15:57:59 +1100 Date: Wed, 7 Feb 1996 15:57:59 +1100 Message-Id: <199602070457.PAA20417@sam.comms.unsw.EDU.AU> X-Sender: m0000256@pop3.unsw.edu.au X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====================_823734098==_" To: chemistry@www.ccl.net From: Xiaoming Zheng Subject: MS-Window as Unix X-terminal X-Attachments: D:\MAIL\XTER.DOC; --=====================_823734098==_ Content-Type: text/plain; charset="us-ascii" Hello, everyone: Many thanks to those who answered my question a few days ago. Attached please find the summary of these answers. Best wishes! 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E-mail: Xiaoming.Zheng@unsw.EDU.AU --=====================_823734098==_-- From amasunov@shiva.Hunter.CUNY.EDU Wed Feb 7 02:56:06 1996 Received: from hcrelay.hunter.cuny.edu for amasunov@shiva.Hunter.CUNY.EDU by www.ccl.net (8.6.10/950822.1) id CAA13792; Wed, 7 Feb 1996 02:49:31 -0500 Received: from shiva.hunter.cuny.edu (amasunov@shiva.hunter.cuny.edu [146.95.128.96]) by hcrelay.hunter.cuny.edu (8.6.12/george0995) with SMTP id CAA06470; Wed, 7 Feb 1996 02:53:41 -0500 Date: Wed, 7 Feb 1996 02:50:08 -0500 (EST) From: Artem Masunov To: Rosina Noto cc: Computational Chemistry List Subject: RE: software to analize normals mode Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Beside MolDen by Gijs Schaftenaar, there is another fresh program which can visualize vibrations - MovieMol by Kersti Hermansson and Lars Ojamae. It is obtainable from authors in executable form for PC, RISC/6000 and Indigo. It uses its own input and works pretty fast. Program to convert G92 output into MovieMol output is obtainable from authors upon request in the form of FORTRAN source. MovieMol is described in http://chem-www.mps.ohio-state.edu/~lars/moviemol.html This homepage has pointers onto other visualization programs. Artem __ _________ / \ / _ _ \ Artem Masunov - amasunov@shiva.hunter.cuny.edu / \\ \\ \\ \ Chemistry Department, Hunter College / /\ \\ \\ \\ \ City University of New York / ____ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 /__/\__/\__\\__\\__\\__\ Tel: (212) 725-0317, Fax: (212) 772-5332 \__\/ \/__//__//__//__/ From chrmiri@techunix.technion.ac.il Wed Feb 7 03:11:03 1996 Received: from techunix.technion.ac.il for chrmiri@techunix.technion.ac.il by www.ccl.net (8.6.10/950822.1) id CAA13765; Wed, 7 Feb 1996 02:48:04 -0500 Received: from tx.technion.ac.il (chrmiri@tx.technion.ac.il [132.68.1.28]) by techunix.technion.ac.il (8.6.12+/8.6.10) with ESMTP id JAA21017; Wed, 7 Feb 1996 09:47:52 +0200 Received: by tx.technion.ac.il (8.6.12+) id JAA19613; Wed, 7 Feb 1996 09:47:52 +0200 Date: Wed, 7 Feb 1996 09:47:52 +0200 (EET) From: Miri Karni To: Rosina Noto cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:G:software to analize normals mode In-Reply-To: <9602061125.AA15197@risc2.iaif.pa.cnr.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try XMOL Miri ****************************************************************************** Dr. Miri Karni Department of Chemistry Technion - Israel Institute of Technology Haifa 32000 Israel e-mail: chrmiri@tx.technion.ac.il FAX:972-4-233735 PHONE:972-4-292699 ****************************************************************************** On Tue, 6 Feb 1996, Rosina Noto wrote: > Dear Collegueas, > I' am looking for a program to analize the normals mode of molecules (starting > from the output og frequencies of G92). > Does anyone have access to such a program? Thanks in advance. > Rosina Noto > ************************** > Dr. R. Noto > Natl Res Council > Inst Interdisciplinary Applicat Phys > Via Archirafi 36 > I- 90123 PALERMO ITALY > ************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: rosa@risc2.iaif.pa.cnr.it > -- Original Sender From: Address: rosa@risc2.iaif.pa.cnr.it > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From amir@genie.terra.co.il Wed Feb 7 05:11:06 1996 Received: from genie.terra.co.il for amir@genie.terra.co.il by www.ccl.net (8.6.10/950822.1) id FAA15026; Wed, 7 Feb 1996 05:09:56 -0500 Received: from merlin.terra.co.il (merlin.terra.co.il [194.90.101.41]) by genie.terra.co.il (8.6.12/8.6.12) with SMTP id KAA14674; Wed, 7 Feb 1996 10:06:38 GMT Date: Wed, 7 Feb 1996 12:08:44 +0200 (IST) From: Amir Gil X-Sender: amir@merlin.terra.co.il To: BBS CHARMM cc: CHEMISTRY@www.ccl.net Subject: trajectory files - summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello netters! Yesterday I sent a question concernning the translation of trajectory files from ALPHA machine to SGI machine. I got plenty of answers and I want to summarize them for you. I will put in only the most usefull ones, to make it short. Thanks to all the reponders, for their time and help. Amir ############################################################################ From: Steve Lionel 06-Feb-1996 0914 -0500 To: amir@genie.terra.co.il Subject: RE: binary files on SGI and ALPHA processors Compile with -convert big_endian. The Alpha is a "little endian" byte order machine, while the SGI is "big endian". This refers to whether the least significant bits are in the lowest addressed byte (little endian) or highest addressed byte (big endian). If you specify -convert big_endian on the command line, DEC Fortran will read and write binary data files using big endian format. You can also select big_endian for specific units - for further information, please see the appendix on "Converting Unformatted Numeric Data" in the DEC Fortran User Manual. Steve ############################################################################ From: Walter Polkosnik To: amir@genie.terra.co.il Cc: chemistry@www.ccl.net Subject: Re: CCL:CHARMm trajectory files-difference between SGI and alpha outputs Different computer architectures store data differently, because of microprocessor hardware details. In order to convert your DEC files to SGI, you first must use the DYNA FORM command on the DEC DCD files to convert the files to text (DHX) format. You then need to ftp those files to the SGI and run the text files through DYNA UNFORM in CHARMm. I have done this before to convert Cray files to SGI files. If you need ore information I can send you my CHARMm input files that do this. ############################################################################ From: "Eldbjoerg S. Heimstad" To: Amir Gil Subject: Re: CCL:CHARMm trajectory files-difference between SGI and alpha outputs Hi, Here is an example script file for converting DCD files to DHX files (formatted) : --------- * Converting binary dcd-files to formatted dhx-files * Remember to convert the dhx-files to dcd files on your * personal machine OPEN READ UNIT 11 FILE NAME "/tmp2/eldbjorg/AMINO.BIN" READ RTF UNIT 11 FILE CLOSE UNIT 11 OPEN READ UNIT 02 FILE NAME "/tmp2/eldbjorg/PARM.BIN" READ PARAMETERS UNIT 02 FILE CLOSE UNIT 02 open read unit 07 card name str_34a.psf read psf card unit 07 close unit 07 OPEN READ UNIT 08 CARD NAME str_34a_min.pdb read coor pdb unit 08 close unit 08 OPEN READ UNIT 50 FILE NAME "str34_300k_260-300.dcd" open write unit 61 card name "str34_300k_260-300.dhx" dyna form first 50 nunit 1 output 61 STOP ------------------------------- And here is an example of converting DHX-files to DCD-files: ------------------------- OPEN READ UNIT 11 FILE NAME $CHM_DATA/AMINO.BIN READ RTF UNIT 11 FILE CLOSE UNIT 11 OPEN READ UNIT 02 FILE NAME $CHM_DATA/PARM.BIN READ PARAMETERS UNIT 02 FILE CLOSE UNIT 02 OPEN READ UNIT 12 CARD NAME $CHM_DATA/MASSES.RTF READ RTF UNIT 12 CARD APPEND CLOSE UNIT 12 OPEN READ UNIT 77 CARD NAME $CHM_DATA/IONS.RTF READ RTF CARD UNIT 77 APPEND CLOSE UNIT 77 open read unit 07 card name str_34a.psf read psf card unit 07 close unit 07 OPEN READ UNIT 08 CARD NAME str_34a_min.pdb read coor pdb unit 08 close unit 08 OPEN READ UNIT 50 CARD NAME str34_300k_140-180.dhx open write unit 61 file name str34_300k_140-180.dcd dyna unform input 50 output 61 STOP ------------------------- Good luck, ####################################################### # Eldbjoerg Sofie Heimstad # # Protein Crystallography Group # # University Of Tromsoe, IMR # # 9037 Tromsoe, NORWAY phone: +47-776-45706 # # +47-776-44737 # # fax : +47-776-44765 # # E-mail: Eldbjorg.Heimstad@chem.uit.no # # URL: http://www.chem.uit.no/KJEMI/heimstad.html # ####################################################### ############################################################################ That's about it Thank you all Amir !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Amir Gil ! ! Chemical and Application engineer ! ! Terra Computers ! ! Ashuah 6 st. ! ! Omer ! ! ISRAEL 84965 ! ! Tel. 07-467502 ! ! Fax. 07-467475 ! ! E-Mail amir@genie.terra.co.il ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! From silviu@chemib5.tau.ac.il Wed Feb 7 09:11:08 1996 Received: from chemib5.tau.ac.il for silviu@chemib5.tau.ac.il by www.ccl.net (8.6.10/950822.1) id JAA17103; Wed, 7 Feb 1996 09:05:20 -0500 Received: by chemib5.tau.ac.il (AIX 3.2/UCB 5.64/4.03) id AA20463; Wed, 7 Feb 1996 15:53:38 +0100 Date: Wed, 7 Feb 1996 15:53:37 +0100 (NFT) From: Zilberman Silviu To: CHEMISTRY@www.ccl.net Subject: MatCad for unix (x11) ? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello netters, I was looking but I couldn't find any unix mathematical software that is as comfortable and easy to use as MatCad. Does anybody knows about a version of MatCad for unix, or similar softwares, that allows the presentation of graphics and calculations on the same screen? I'll summerize the answers. Silviu Zilberman **************************************************** * Silviu Zilberman * * Tel - Aviv University * * Faculty of Exact Sciences, Chemistry department * * Israel * * * * E-mail: silviu@chemib5.tau.ac.il * **************************************************** From dgregory@biosym.com Wed Feb 7 11:41:09 1996 Received: from nic.cerf.net for dgregory@biosym.com by www.ccl.net (8.6.10/950822.1) id LAA19148; Wed, 7 Feb 1996 11:35:36 -0500 Received: from biff.biosym.com (biff.biosym.com [146.202.0.225]) by nic.cerf.net (8.7.3/8.6.9) with SMTP id IAA23371; Wed, 7 Feb 1996 08:35:30 -0800 (PST) Received: from [146.202.16.4] by biff.biosym.com (4.1/SMI-4.1) id AA19064; Wed, 7 Feb 96 08:31:17 PST Message-Id: <9602071631.AA19064@biff.biosym.com> Date: Wed, 7 Feb 1996 08:36:30 -0500 To: charmm-bbs@emperor.harvard.edu, chemistry@www.ccl.net From: dgregory@biosym.com (Don Gregory) X-Sender: dgregory@146.202.0.225 Subject: Re: CHM! CHARMm trajectory files-difference between SGI and alpha outputs Hi everyone, just a subtle clarification: At 9:06 AM 2/6/96 +0200, Amir Gil wrote: >I have a problem reading trajectory binary files.The files are produced by >CHARMm (v23f3) on DEC ALPHA machine, and I am trying to read them on SGI >INDY machine. The current commercial version of CHARMm v23.2 has been compiled on the DEC with the " -convert big_endian" flag, just to avoid this problem. I hope I'm right is thinking that Amir is actually referring to the use of CHARMM v23.3 the current academic version (the update of which we at MSI plan to provide commercially soon)! Don Gregory From res@inorg.chem.ethz.ch Wed Feb 7 13:11:10 1996 Received: from bernina.ethz.ch for res@inorg.chem.ethz.ch by www.ccl.net (8.6.10/950822.1) id NAA20286; Wed, 7 Feb 1996 13:10:34 -0500 Received: from inorg.chem.ethz.ch (actually tintin.ethz.ch) by bernina.ethz.ch with SMTP inbound; Wed, 7 Feb 1996 19:09:47 +0100 Received: by inorg.chem.ethz.ch (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id TAA01112; Wed, 7 Feb 1996 19:04:49 +0100 From: Andreas Eggenschwiler Message-Id: <9602071904.ZM1110@tintin.ethz.ch> Date: Wed, 7 Feb 1996 19:04:48 +0100 Reply-To: res@inorg.chem.ethz.ch X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@www.ccl.net Subject: AIM surfaces with G94 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers We are trying to calculate and visualize AIM zero flux surfaces. For the visualisation we would like to use AVS, for the calculation the AIM module of Gaussian 94 (l609). The Atomic_Surfaces option of the AIM keyword seams to be supposed to compute AIM surfaces, however we did not figure out how it works and what it exactly does. The zero flux surfaces seam to be written to the disk into the .rwf file by l609, however we do not know how to recover them and I do not really feel like hacking the G94 source code. Does anybody have a suggestions? Thanks in advance Res From owner-chemistry@ccl.net Wed Feb 7 16:26:13 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id QAA24467; Wed, 7 Feb 1996 16:13:16 -0500 Received: from CHEMRES.CHEM.CORNELL.EDU for tang@Xtended.chem.cornell.edu by bedrock.ccl.net (8.7.1/950822.1) id QAA03423; Wed, 7 Feb 1996 16:13:13 -0500 (EST) From: Received: from XTENDED.CHEM.CORNELL.EDU by CHEMRES.CHEM.CORNELL.EDU with SMTP (1.36.108.10/15.6) id AA23969; Wed, 7 Feb 1996 16:10:59 -0500 Received: (from tang@localhost) by Xtended.chem.cornell.edu (8.7.1/8.7.1) id QAA17408; Wed, 7 Feb 1996 16:10:15 -0500 Date: Wed, 7 Feb 1996 16:10:15 -0500 Message-Id: <199602072110.QAA17408@Xtended.chem.cornell.edu> To: chemistry@ccl.net Subject: solvent effect on electronic spectra - summary Hi, there! Here is the summary of the messages I got in response to my previous message about solvent effect on the electronic spectra. Many thanks to everybody who kindly replied my query. In addition to the literature provided by the enclosed messages, I also found a chapter on the same subject in the old book "Molecular Interactions and Electronic Spectra" by N. Mataga and T. Kubota (1970, Dekker). It's kind of old, but the review delivers some theoretical background. Again, thank you all for the help. Happy computing! Huang TANG -Cornell Quantum Therapy Center for Molecules and Solids :-) *********************** my original message ************************* I was asked lately by someone who was interested in theoretical studies on solvent effect on the electronic transitions of organic compounds. Could you guys point me to recent publications on this subject? ************************* summary of replies ************************ From: Sergio Nuzzo look up the following article: B. Brunschwig, S. Ehrenson and N. Sutin J. Phys. Chem. 1987 (91) 4717-4723 sergio ------------------------------------------------------------------------ From: imcvey@en.com (Iain McVey) Here are some references that I have Blair et. al. JACS 1986, 111, 6948-6956 Blair et. al. J Physical Chemistry 1990, 94, 4470-4476 Luzhkov and Warshel JACS, 1991, 113, 4491-4499 Karelson and Zerner J Phys Chem 1992, 96, 6949-6957 I'm plannig to do my Prop Oral on a similar project so I may be able to tell you more in a few months if you're still interested then drop me a line and I'll send you a copy of my literature review. Assuming that what I wnat to propose has not already been done :) hope this helps Iain ------------------------------------------------------------------------ From: YONG HUANG I use COSMO model so I can give you two important papers papers on this. A.Klamt and G.Schuurmann, "COSMO: A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and its Gradient", J.Chem.Soc.Perkin Trans. 2, 1993. A.Klamt, "Conductor-like Screening Model for Real Solvents: A New Approach to the Quantitative Calculation of Solvation Phenomena", J.Phys.Chem., 99, 2224, 1995. ------------------------------------------------------------------------ From: "Ernest Chamot" Hi Huang, It's not specifically the electronic transitions that you asked about: But some of Chris Cramer's work shows strikingly good results in modeling solvent effects, not only on the geometry and energy, but also the electronic distribution with the SM-2 solvation model. I have had similar good results with the COSMO model in Mopac. Cramer's most recent results appeared in ECTOC-1 as paper #46, "Predicting Regioselectivity in the Reduction of Polynitroaromatiocs in Aqueous Solution." This was also submitted for hardcopy publication recently, but I don't have that reference. Cris's email address is: cramer@maroon.tc.umn.edu For Andreas Klamt's development of COSMO, check out: J. Phys. Chem. 1995, 99, 2224. I hope this helps. Ernest Chamot ------------------------------------------------------------------------ From: "Ferenc Molnar" Hi! Take a look at Volume 7 of the "Reviews in Computational Chemistry", Lipkowitz, Boyd (Eds.). There is a review about combined "QM/MM/MD" methods that deals with solvent effects on electronic transitions. Cheers, Ferenc ------------------------------------------------------------------------- From: Gerd Thys Well, I tried this type of calculations once... I used the semi-empirical AM1 method as implemented in MOPAC. To simulate the solvent, I used the COSMO method (also implemented in MOPAC). I must say the calculated solvent effects aren't that big in my case, but I can imagine that when you have a molecule with a big difference in dipole moment in ground-state and excited state these influences get much bigger... In fact it was just a try-out... If you want to read more about it, you can look at the paper I prepared for the 2nd Electronic Comp. Chem. Conference (ECCC2)... It's in review now, but it's still on-line... http://sch-www.uia.ac.be/u/thys/eccc2/paper.html A comprehensive overview of solvent effects (including calculations of all kind) can be found in 'Solvent and Solvent Effects in Organic Chemistry' by Christian Reichardt VCH Verlag, Weinheim, 1990 (2nd ed) ISBN 3-527-26726-3 If you get more replies, please forward to me... Best regards, Gerd -------------------------------------------------------------------------- From: A.H.deVries@dl.ac.uk (Alex de Vries) Dear Huang TANG, I got your query on solvent effects on spectra from a friend of mine and I think I can help you with a few references: Some theory in: Theory of Solvent Effects on Electronic Spectra, H. Agren and K.V. Mikkelsen J. Mol. Struct. (THEOCHEM) 234, 425-467 (1991) Theory and Application: A.H. de Vries. P.Th. van Duijnen and A.H. Juffer Int. J. Quant. Chem., Quant. Chem. Symp. 27, 451-466 (1993) A.H. de Vries and P.Th. van Duijnen Int. J. Quant. Chem. 1995 or 1996 (should be out by now) "Solvatochromism of the pi*<-n transition of acetone by combined quantum mechanical-classical mechanical calculations" J.T. Blair, K. Krogh-Jespersen and R.M. Levy J. Am. Chem. Soc. 111, 6948-6956 (1989) S.E. DeBolt and P.A. Kollman J. Am. Chem. Soc. 112, 7515-7524 (1990) V. Luzhkov and A. Warshel J. Am. Chem. Soc. 113, 4491-4499 (1991) J. Gao J. Am. Chem. Soc. 116, 9324-9328 (1994) M. Karelson and M.C. Zerner J. Am. Chem. SOc. 112, 9405-9406 (1990) N. Roesch and M.C. Zerner J. Phys. Chem. 98, 5817-5823 (1994) I hope these will give you enough lead to dive into this fascinating subject. Alex de Vries From raman@bioc01.uthscsa.edu Wed Feb 7 23:56:18 1996 Received: from elzip.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/950822.1) id XAA28851; Wed, 7 Feb 1996 23:44:34 -0500 Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V5.0-5 #13300) id <01I0Y3KKIXF4002PFZ@uthscsa.edu> for chemistry@www.ccl.net; Wed, 07 Feb 1996 21:47:42 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA08625; Wed, 07 Feb 1996 21:45:56 -0600 (CST) Date: Wed, 07 Feb 1996 21:45:53 -0600 (CST) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: Imidazole binding to Heme To: chemistry@www.ccl.net Message-id: <9602080345.AA08625@bioc01.uthscsa.edu> X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT Dear Netters: I am desperately looking for either theoretical or experimental information on the rate of imidazole binding by heme or heme peptide. I am not aware of any work in this area since 1967 and any information you can provide will be very helpful. I am not interested in the interaction of imidazole with native proteins. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/