From chemistry-request@server.ccl.net Tue Dec 7 19:07:56 1999 Received: from teapot32.domain8.bigpond.com (teapot32.domain8.bigpond.com [139.134.5.180]) by server.ccl.net (8.8.7/8.8.7) with SMTP id TAA29490 for ; Tue, 7 Dec 1999 19:07:54 -0500 Received: from localhost (localhost [127.0.0.1]) by teapot32.domain8.bigpond.com (NTMail 3.02.13) with ESMTP id aa555906 for ; Wed, 8 Dec 1999 08:59:01 +1000 Received: from BDIP-T-010-p-102-30.tmns.net.au ([139.134.102.30]) by mail8.bigpond.com (Claudes-Caring-MailRouter V2.6h 17/531580); 08 Dec 1999 08:58:59 Message-ID: <002201bf4107$000a6140$108b67cc@hnlsyd8> From: "Dr Huang" To: , , Subject: Re: download new version of electrochemistry software POLAR 4 X-Mailer: Microsoft Outlook Express 5.00.2314.1300 Date: Wed, 8 Dec 1999 10:01:25 +1100 Would you please read FAQ in its document? FAQ says: Q: Where can I download these dll? A: Microsoft Visual Basic 6 runtime DLL files are from http://www.simtel.net/simtel.net/win95/dll.html, where msvbvm60.dll is inside simvb6-3.zip. Microsoft Visual Basic 4 16-bit runtime DLL files are >from http://www.simtel.net/simtel.net/win3/dll.html. -------------------------------- Hello! I just tried to run Polar 4 on Win95. Unfortunately program couldn't run with the error that MSVBVM60.DLL was not found. Do you know by any chance where can I get this file from? Thanks very much for your help Miroslava At 02:30 PM 12/7/1999 +1100, you wrote: > > Polar 4 for Windows: Electrochemical simulation and data analysis > >[IN CCL: http://www.ccl.net/cca/software/MS-WIN95-NT/Polarograms ] > > DrHuang Pty Ltd >124 Eastern Avenue, Kingsford, Sydney, NSW 2032, Australia >Phone: 61 2 96620516, 0413 008 019 >mailto:polarography@bigFoot.com, showing@bigFoot.com >www.electrochem.net >www.DrHuang.net >www.electroanal.com > > It analytically and digitally simulates voltammograms (polarograms) >at 8 electrode geometries (planar, spherical, semi- >spherical, cylindrical, semi-cylindrical, microdisc, thin film, and rotating >electrodes) in over 5 techniques (linear sweep and CV, DC, normal pulse, >differential pulse, and square wave voltammetries). It outputs current, >resistance, conductivity and surface concentration. It also simulates >effects >of charge current, resistance, noise, electrolyte, stripping time, stripping >potential, etc. User can type in his mechanism. > > It analyses any ASCII x-y data for detecting peak location, peak >value, semi-derivative, derivative, intergral, semi-intergral, curve >fitting, >and separating overlapped peaks. > > It shows a tip when the user put mouse cursor over a lable. It can >separate overlapped voltammograms into individuals, and extract real peaks >>from voltammogram with noise and baseline. Users can compare by the >theoretical peak values, analytically and digitally simulation, and choose >to extract which kinetic pararmeters. Its data can be imported into other >program (e.g. MS Excel). > > It has been successfully applied to fit experimental >polarograms (voltammograms) of In(III), Cd(II), Pb(II), Tl(I), Cr(III). >Zn(II), and binuclear copper complex in aqueous and non-aqueous media >at mercury, solid metal and non-metal electrodes (specifically the >dropping mercury, hanging mercury drop, gold, platinum and glassy >carbon electrodes) by various electrochemical techniques (differential >pulse, square wave, and pseudo-derivative normal pulse polarographies). > > It is available from the author or download from my Web site. > > > > > > > ___________________________________________________________ Miroslava Cuperlovic-Culf, e-mail: mculf@mta.ca tel. 506-364-2411 http://www.mta.ca/faculty/science/chem/staff/mculf.htm ____________________________________________________________ Dr Huang wrote in message news:feJ24.5799$5K1.22843@newsfeeds.bigpond.com... > Polar 4 for Windows: Electrochemical simulation and data analysis > > DrHuang Pty Ltd > 124 Eastern Avenue, Kingsford, Sydney, NSW 2032, Australia > Phone: 61 2 96620516, 0413 008 019 > mailto:polarography@bigFoot.com, showing@bigFoot.com > www.electrochem.net > www.DrHuang.net > www.electroanal.com > > It analytically and digitally simulates voltammograms (polarograms) > at 8 electrode geometries (planar, spherical, semi- > spherical, cylindrical, semi-cylindrical, microdisc, thin film, and rotating > electrodes) in over 5 techniques (linear sweep and CV, DC, normal pulse, > differential pulse, and square wave voltammetries). It outputs current, > resistance, conductivity and surface concentration. It also simulates > effects > of charge current, resistance, noise, electrolyte, stripping time, stripping > potential, etc. User can type in his mechanism. > > It analyses any ASCII x-y data for detecting peak location, peak > value, semi-derivative, derivative, intergral, semi-intergral, curve > fitting, > and separating overlapped peaks. > > It shows a tip when the user put mouse cursor over a lable. It can > separate overlapped voltammograms into individuals, and extract real peaks > from voltammogram with noise and baseline. Users can compare by the > theoretical peak values, analytically and digitally simulation, and choose > to extract which kinetic pararmeters. Its data can be imported into other > program (e.g. MS Excel). > > It has been successfully applied to fit experimental > polarograms (voltammograms) of In(III), Cd(II), Pb(II), Tl(I), Cr(III). > Zn(II), and binuclear copper complex in aqueous and non-aqueous media > at mercury, solid metal and non-metal electrodes (specifically the > dropping mercury, hanging mercury drop, gold, platinum and glassy > carbon electrodes) by various electrochemical techniques (differential > pulse, square wave, and pseudo-derivative normal pulse polarographies). > > It is available from the author or download from my Web site. > > > From chemistry-request@server.ccl.net Wed Dec 8 06:13:21 1999 Received: from kalium.kiku.dk (kalium.kiku.dk [130.225.100.59]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA31929 for ; Wed, 8 Dec 1999 06:13:20 -0500 Received: from [130.225.100.105] (helo=[130.225.100.105]) by kalium.kiku.dk with smtp (Exim 2.12 #1) id 11vdxN-0007NP-00 for CHEMISTRY@ccl.net; Wed, 8 Dec 1999 11:04:22 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 8 Dec 1999 12:32:49 +0100 To: CHEMISTRY@ccl.net From: theis@kalium.kiku.dk (Theis Soelling) Subject: Transition States for Reactions with no Activation Barrier Dear All, A few days ago Balakrishnan Viswanathan inquired about methods for characterizing transition states in reactions without an activation barrier. One approach to this problem is to use variational transition state theory (VTST) in which the minimum in flux along the reaction coordinate is associated with the transition state of the reaction. A nice description of the actual procedure can be found in Hase, W. L. Acc. Chem. Res. 1983, 16, 258 and Baer, T.; Hase, W. L. Unimolecular Reaction Dynamics; Theory and Experiments, Oxford University Press: Oxford, 1996; pp. 256. There are at least three (free) programs that can perform VTST-calculations: HYDRA, UNIMOL and POLYRATE. In this manner, I have characterized the transition states of a substantial amount of unimolecular dissociation reactions of microcanonical ensembles. I have found that the position of the flux minimum moves towards the products as I decrease the excess energy of the reactant. Also, I have found that when a reactant with a given internal energy dissociates via two (related) competing exit channels, the flux minimum is found later on the reaction coordinate for the exit channel with the higher dissociation energy. Does anybody know the formal reasons for these observations? Cheers, Theis ** ** ** ** Mr. Theis Ivan Solling ** ** ** ** ** Department of Chemistry ****** ****** University of Copenhagen ** ** ** DK-2100 Copenhagen ** ** ** Ph. ++45-3532-0187/Fax. ++45-3532-0212 From chemistry-request@server.ccl.net Wed Dec 8 11:18:16 1999 Received: from lambda.inrs.uquebec.ca (lambda.inrs.uquebec.ca [207.162.3.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA01222 for ; Wed, 8 Dec 1999 11:18:16 -0500 Received: from iaf.uquebec.ca ([207.162.6.37]) by lambda.inrs.uquebec.ca (Netscape Messaging Server 3.62) with ESMTP id 360; Wed, 8 Dec 1999 10:08:02 -0500 Message-ID: <384E7684.2956EE39@iaf.uquebec.ca> Date: Wed, 08 Dec 1999 10:17:24 -0500 From: "Jianhui Wu" To: chemistry@ccl.net, tjm@spawn.scs.uiuc.edu, sangeeta@bioinfo.ernet.in Subject: Summary: InsightII, PBC, Counter ions, Protein Dear all, Last week I asked a question regarding how to add counter ions in a PBC discovery calculation. I would like to thank Dr. Marek Orzechowski and Dr. Eberhard von Kitzing for their advice. This is the only two advice I got up to now. If you have more advice, please direct it to me. I will summarize them again if I get more response. Regards, Jian Hui Wu ************************************************************* Original question: > Dear all, > > I am trying to model ligand-protein interaction using discovery within > InsightII (version 97). I would like to solvate the system by PBC water > box. The protein has –12 charge (ligand is neutral). Is it essential to add > the counter ions in the system to neutralize the net charge before >a PBC discovery calculation (MM or MD) is performed? (Probably, yes) > > I find counter_ion.bcl in the $BIOSYM/gifts/insight/BCL/ directory. > It is for DNA stuff. It seems that 12 Na+ ions have to be put into the > 12 most negative charged position (somewhere in the protein, I guess), > how can I find these position? > > Any help will be greatly appreciated. > ************************************************************* Advice: (1) Eberhard von Kitzing The Maxwell relaxation time (see introductions into semi conductor physics) is the time needed by the system to equilibrate. It is in the order of lDH^2/D where lDH is the Debye length and D the diffusion constant of the ions. Thus, to add salt in addition to the excess charge would improve the equilibration of your simulation. Test calculations done by others showed that such additional salt generally stabilizes the simulation. ************************************************************** (2) Marek Orzechowski ...As far as I understood your problem is connected with positions of counterions in a cell.I am just curious whether You had no problems with assigning charges because this was my problem.I didn't use counter_ion.bcl file, but took one atom of Na ,put charge +1 on it and tried to assign charge,potential and partial charge using forcfield pulldown.And it didn't work. But returning to your problem I think that You don't have to bother about positionning Na+ ions ,because during minimization they find the best positions.This is my personal opinion ,but seems to be resonable.What do You think?Attraction between Na+ and charged groups in protein is strong enough to place Na+ in right positions. You have to ,of course fix the protein first. Remember of the value of cutoff You use for electrostatic interactions. I can advise You not to use the file *.bcl ,but did somthig what I have done. Take one atom of Na, using forcfield pulldown assign everything, what is needed (probably You'll see: Warning!Total formal charge is not equal partial charge or something simmilar - it depends on the forcefield You use), then take 12 atoms of Na (as You need) and do the same putting them first in the cell wherever You want. Assign charges and potential types and edit files *.mdf and *.car writting 1+ instead of 0 (in the positions of charges of Na+),how it is after doing as described above (if You had the warning ,of course ,if not Your're lucky and You don't have to edit anything). Best wishes , Marek ************************************************************* E.O.F From chemistry-request@server.ccl.net Wed Dec 8 16:58:01 1999 Received: from mlx4.unm.edu (qmailr@mlx4.unm.edu [129.24.10.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA02847 for ; Wed, 8 Dec 1999 16:58:01 -0500 Received: (qmail 26627 invoked from network); 8 Dec 1999 20:49:00 -0000 Received: from bldg227-0214.unm.edu (HELO Jayhalk?1.unm.edu) (129.24.163.41) by mlx4.unm.edu with SMTP; 8 Dec 1999 20:48:59 -0000 Message-Id: <4.2.0.58.19991208134228.009e7360@mail.unm.edu> X-Sender: jborn@mail.unm.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Wed, 08 Dec 1999 13:47:10 -0700 To: chemistry@ccl.net From: "Jerry L. Born" Subject: Software selection Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All I am interested in modeling the interaction of hematin with drug molecules. I have attempted this work with several packages but without "success". The theory states that antimalarial agents bind via pi/pi bonding and the interaction of a charged ammonium with the carboxyl side chains of hematin, sort of like an open faced sandwich. Please suggest a modeling package for PC or SGI that might produce useable information. thanks jlb Jerry L. Born, Ph.D. Voice 505-272-3657 Professor of Pharmacy (Med. Chem./Toxicology) The University of New Mexico FAX 505-272-6749 College of Pharmacy 2502 Marble NE Albuquerque, NM 87131 From chemistry-request@server.ccl.net Wed Dec 8 19:10:06 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA03500 for ; Wed, 8 Dec 1999 19:10:06 -0500 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id OAA04890 for ; Wed, 8 Dec 1999 14:59:04 -0800 (PST) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0) with SMTP id OAA452398 for ; Wed, 8 Dec 1999 14:59:04 -0800 (PST) Date: Wed, 8 Dec 1999 14:59:04 -0800 (PST) From: Maneesh Yadav To: chemistry@ccl.net Subject: Autodock + Linux problems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hmm after getting everything running the autodock3 program core dumps during a docking on my intel linux box, the dlg file seems to stop after trying open the first grid map, someone else had these problems too; could they and anybody else who has tried tell me where there dlg files stop? I tried stuff like running with the sqrt option, smaller grids etc., none seems to help.. A run with gdb makes it seem like there is a file trying to be (or is assumed open) where it is not (the error points to _IO_vfscanf)..but I could be totally wrong. BTW If anyone actually does have autodock working under linux, I'd like to know that too.^^^^^^^^^^^^^