From marek@mel.dit.csiro.au Wed Dec 20 04:34:39 1995 Received: from shark.mel.dit.csiro.au for marek@mel.dit.csiro.au by www.ccl.net (8.6.10/950822.1) id EAA15973; Wed, 20 Dec 1995 04:22:23 -0500 Received: from trout.mel.dit.CSIRO.AU by shark.mel.dit.csiro.au with SMTP id AA27225 (5.65c/IDA-1.4.4/DIT-1.3 for chemistry@www.ccl.net); Wed, 20 Dec 1995 20:22:20 +1100 Message-Id: <199512200922.AA27225@shark.mel.dit.csiro.au> To: CHEMISTRY@www.ccl.net Subject: Spend few hot days in Melbourne, Australia Date: Wed, 20 Dec 1995 20:22:20 +1100 From: "Marek T. Michalewicz" This is your chance to reword yourself with few fascinating days filled with warm summer weather and the break-through expositions of the recent advances in computational biology, medicine and agriculture. Visit Melbourne! Visit our WWW page before the Year's End! You will find there the full program of invited speakers' lectures, abstracts of their talks as well as a simple registration form. Seasons Greetings, Marek Michalewicz Seasons Greetings, Marek From jagan@cmmacs.ernet.in Wed Dec 20 05:34:40 1995 Received: from relay7.UU.NET for jagan@cmmacs.ernet.in by www.ccl.net (8.6.10/950822.1) id FAA16374; Wed, 20 Dec 1995 05:20:13 -0500 Received: from iisc.ernet.in by relay7.UU.NET with SMTP id QQzuxl24155; Wed, 20 Dec 1995 05:19:46 -0500 (EST) Received: from cmmacs.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA13654; Wed, 20 Dec 95 15:54:43+0530 From: jagan@cmmacs.ernet.in (B Jagannadh) X-Mailer: SCO System V Mail (version 3.2) To: CHEMISTRY@www.ccl.net Subject: Looking for charges for Azidothymidine Date: Wed, 20 Dec 95 15:51:55 IST Message-Id: <9512201551.aa01741@cmmacs.ernet.in> Dear ChemNetters, I have the need to calculate the conformations of AZT and its analogues using AMBER for which I like to have information on the availability of charges for AZT along with information on how the charges were derived. I will be grateful for information. With Regards, B.Jagannadh email:jagan@cmmacs.ernet.in From VARNAI@ch.bme.hu Wed Dec 20 09:49:47 1995 Received: from ns.bme.hu for VARNAI@ch.bme.hu by www.ccl.net (8.6.10/950822.1) id JAA18986; Wed, 20 Dec 1995 09:43:36 -0500 Received: from ch.bme.hu (ch.bme.hu [152.66.64.1]) by ns.bme.hu (8.6.12/8.6.12) with SMTP id PAA23604 for ; Wed, 20 Dec 1995 15:43:32 +0100 Received: from CH/TEMPQ by ch.bme.hu (Mercury 1.12); Wed, 20 Dec 95 15:49:11 +1100 Received: from TEMPQ by CH (Mercury 1.12); Wed, 20 Dec 95 15:48:59 +1100 From: "Varnai Peter" To: chemistry@www.ccl.net Date: Wed, 20 Dec 1995 15:48:49 GMT+100 Subject: Internal Rotation X-Confirm-Reading-To: "Varnai Peter" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <12668554497@ch.bme.hu> Dear CCLers, I would like to hear how people usually handle low energy internal rotations appearing among harmonic frequencies? Is the following a not-very-bad approach to correct this problem: 1, check the low frequency dihedral motions to assign the internal rotations. 2, subtract these energy contributions from ZPE. 3, thermal energy part of the total energy could be 1/2kt for these motions (classical). In case the Gibbs free energy is needed: 4, calculating with a statistical mechanics formula for the "sum over states" for these motions. Please respond me directly, I will surely send the summary to all! Peter Varnai PhD student varnai@ch.bme.hu From sg928ah5@dunx1.ocs.drexel.edu Wed Dec 20 19:49:51 1995 Received: from dunx1.ocs.drexel.edu for sg928ah5@dunx1.ocs.drexel.edu by www.ccl.net (8.6.10/950822.1) id TAA26665; Wed, 20 Dec 1995 19:43:45 -0500 Received: (from sg928ah5@localhost) by dunx1.ocs.drexel.edu (8.7.3/8.6.12) id TAA12686 for chemistry@www.ccl.net; Wed, 20 Dec 1995 19:41:55 -0500 (EST) From: James Ianni Message-Id: <199512210041.TAA12686@dunx1.ocs.drexel.edu> Subject: New, Powerful kinetics program:KINTECUS To: chemistry@www.ccl.net Date: Wed, 20 Dec 1995 19:41:55 -0500 (EST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text immi mmmi mmmi mmi mm mmmmmmmmmi immmmmmmmmi ,mmm_ i mmm mm gmms . @[ iP @[ ]YW. ] P ]@[ [ '@@ ` ,Z! V[ ]@ ] ,A V[ @[ gf @[ ]'@b ] ]@[ @@ ]@` ! ]@ ] W ! @[ gf @[ ] Y@. ] ]@[ @@ W@ ]@ ] MW. @[d! @[ ] !@W ] ]@[ @@ , @A ]@ ] !M@s_ @@b @[ ] ]@i ] ]@[ @@mmmW @[ ]@ ] VM@W. @PMm @[ ] '@W ] ]@[ @@ ' @[ ]@ ] ~M@m @['MW. @[ ] V@i] ]@[ @@ M@ ]@ ] Y@i @[ M@. @[ ] M@] ]@[ @@ ]@. !@. ] @[ @[ Y@. @[ ] ]@@ ]@[ @@ ]b i` MW [ ] @ ,@b. ,@W_ mmmi d_ M@ ,d@b. ,g@@______i V+___=/ '*+___/ !=c___/f "The Ultimate Kinetics Program Module" Kintecus (c) Copyright 1995 James C. Ianni. All Rights Reserved. For :PC (=>MS-DOS 3.3) Subject:Chemistry, Physics & Engineering Type :DISABLED Shareware [ Introduction ] ============================================================================= Kintecus is a program to model the reactions of chemical, biological, nuclear and atmospheric processes using two input spreadsheet files: a reaction spreadsheet and a species description spreadsheet. Kintecus can model like no other modeler can. Absolutely NO programming, compiling nor linking required. A quick overview of the main features are: 1) the ability to model over 2,000 reactions in less than 8 megabytes of RAM running in pure high speed 32-bit under DOS! (And because the program is *ENTIRELY* written in ANSI-FORTRAN 77, other platforms, AIX, Cray, Sun, Mac and Amiga are coming...) 2) the ability to use concentration profiles of any wave pattern for any species or laser profile for any hv. This is very useful for studying very complicated external perturbation affects or using your own experimentally recorded concentration profile in your model. 3) a powerful parser with mass & charge balance checker for those reactions that the OCR or the graduate student "supposedly" entered in correctly but the model is yielding incorrect results or is divergent. Do you know a kinetics program that can completely parse and check for mass/charge balance on a reaction like this: # # Rate Constants , REACTIONS: # 1.234e-20 , CH3(((NO2)3(CO)93)3(CH2)9)23.30H2O+ + Co2 = A--- + B++++ Or how about this: # # Rate Constants , REACTIONS: # 5.043e+20 , 3.43234 (CH4(N(PO342)43(CH3)3)34)(Os(S7)8)34++++ + 199.432 X++++5CH5+ ==> 5.434Some_Really_Funky_Enzyme_Name_But_I_Just_don't_Remember_IT_This_Name_Is_Ju st_Too_Long_It_Seems_to_go_on_and_on_like_that_a n n o y i n g Rabbit???---- + 8 HCl + HCO3- Kintecus is able to accurately check the above reaction for mass and charge balance because you can create an optional name file containing common names for species and then their mass representation. This smart mass balance can be used for biological and nuclear reactions! Also duplicate reaction and species checking. 4) As you can see in the above reaction, *FRACTIONAL* coefficients for species! Now you can finally model that last step in the Oregonator or crunch 100 elementary reaction steps in one reaction step! 5) Quickly and easily hold one or more concentrations of any species at a constant level just by typing the value in the field of the species. 6) Built in support for photochemical reactions involving hv and Loseschmidt's number. Current units supported are molecules/cm^3, moles/liter & ppm. 7) Model reactions from femtoseconds to years! A special switch in Kintecus allows it to output the concentration of the species that are displayed only if its concentration has changed significantly from its past values. This may seem like no big deal, but if you model reactions that last from days to years you can easily generate files that are dozens of megabytes in size or more. Such a file is nearly impossible or extremely time consuming to plot or print, but in Kintecus a special option turns a 100-multimeg file into a 100 kilobyte file without any loss in data! 8) Automatic generation of the species spreadsheet file using the reaction spreadsheet file. 9) The ability to do reactions in a continuous stirred tank reactor (CSTR) with multiple inlets and outlets. 10) Support for sensitivity analysis. 11) The integration is carried out by an integration technique superior to Gears with all internal matrices (reactions and jacobians) are calculated analytically. There in NO SLOW AND USUALLY UNSTABLE APPROXIMATION[1]. 12) Support for Excel and Lotus spreadsheet programs. A QUICK EXAMPLE OF ENTERING AND RUNNING A SAMPLE KINETICS SCHEME: ----------------------------------------------------------------- Go into MS-DOS and create a file named MODEL.DAT. Enter your reactions like so (using a spreadsheet to do this is highly recommended): 1.323e-4, A- +Widget-- + C==>G+++ + F---+H20 3.2 , E+F = = > G + DNA_A_Replicated_Over_One_Day 54.34 , G = A END ( <==-- Make sure this END is here) Run Kintecus: >Kintecus -c Now copy the created ADDSPEC.TXT file as a SPECIES.DAT file (ie. >COPY ADDSPEC.TXT SPECIES.DAT ) Edit the initial concentration fields in species.dat for your model and type "Y" in the DISPLAY field for species' concentrations you want to save. Run kintecus: >KINTECUS -ig:mass -ig:charge -show. That's all. ----------------------------------------------------------------- From sg928ah5@dunx1.ocs.drexel.edu Wed Dec 20 21:34:52 1995 Received: from dunx1.ocs.drexel.edu for sg928ah5@dunx1.ocs.drexel.edu by www.ccl.net (8.6.10/950822.1) id VAA27171; Wed, 20 Dec 1995 21:20:49 -0500 Received: (from sg928ah5@localhost) by dunx1.ocs.drexel.edu (8.7.3/8.6.12) id VAA20330 for chemistry@www.ccl.net; Wed, 20 Dec 1995 21:19:00 -0500 (EST) From: James Ianni Message-Id: <199512210219.VAA20330@dunx1.ocs.drexel.edu> Subject: KINTECUS -2 To: chemistry@www.ccl.net Date: Wed, 20 Dec 1995 21:18:59 -0500 (EST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text WHERE TO GET: Using Netscape/Webrowser/Mosaic: http://www.ccl.net/chemistry.html under Software/MS-DOS Using FTP: FTP www.ccl.net under pub/chemistry/software/MS-DOS/kintecus (remember to use the same exact case of the letters, and don't forget to get it using binary transfer mode.) example: >FTP www.ccl.net USER:anonymous PASSWORD:(enter your E-mail address) ftp>cd pub/chemistry/software/MS-DOS/kintecus ftp>bi ftp>mget *.* ftp>bye (... 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