From chemistry-request@server.ccl.net Sun Feb 18 02:10:13 2001 Received: from fjohn.Stanford.EDU (fjohn.Stanford.EDU [171.64.38.72]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1I7ADw19207 for ; Sun, 18 Feb 2001 02:10:13 -0500 Received: from localhost (greg@localhost) by fjohn.Stanford.EDU (8.9.3/8.9.3) with ESMTP id XAA22289 for ; Sat, 17 Feb 2001 23:10:16 -0800 Date: Sat, 17 Feb 2001 23:10:16 -0800 (PST) From: Greg Lakatos To: chemistry@ccl.net Subject: DCD File Internals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Does anyone know where I can find a complete description of the internals of the charmm DCD file format (Unfortunately I don't have the charmm source code)? Thank you for the help. - Greg From chemistry-request@server.ccl.net Sun Feb 18 02:53:03 2001 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1I7qsw19281 for ; Sun, 18 Feb 2001 02:53:00 -0500 Received: from iris.sipp.ac.cn [202.127.25.123] by iris.sipp.ac.cn with ESMTP (SMTPD32-6.04) id A137982012A; Sun, 18 Feb 2001 16:00:55 +0800 Sender: user@ccl.net Message-ID: <38ACFA2D.9DFF4405@iris.sipp.ac.cn> Date: Fri, 18 Feb 2000 15:52:13 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: how to solvate a molecule using charmm Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, everyone: I am a new user for charmm, and here are two question that I need some help. I am studying a enzyme about 700 amino acid, and I want to solvate it in water before doing minimization. I am not quite sure how to solve it, I have tried to solvate with tip526.crd, but it only solvate only a part of my enzyme, I am afraid the box is too small to it. So I wonder if there are some one can give me some input examples for generate big box. Another question is that I noticed that there are some reports that introduced the water drople model about solvation, I also wish some one could give me some examples. Hope my questions do not give you too much trouble. Thanks in advance. Regards, mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Sun Feb 18 22:40:34 2001 Received: from melpop01.goconnect.net ([202.92.76.50]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1J3eWw29205 for ; Sun, 18 Feb 2001 22:40:33 -0500 Received: from pentium466 ([202.92.72.127]) by melpop01.goconnect.net (Netscape Messaging Server 4.15) with ESMTP id G8ZJGB00.T3T for ; Mon, 19 Feb 2001 14:38:35 +1100 Message-ID: <004b01c09a2e$119c6850$0100a8c0@pentium466> Reply-To: "DrHuang.com" From: "DrHuang.com" To: Subject: I upload electrochemistry software polar34.zip and polar34a.zip to ccl.net Date: Mon, 19 Feb 2001 14:40:11 +1000 Organization: DrHuang.com MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Polar 4.3 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 Fax: 61 2 93138266 mailto:polar@electroanal.com, polar@DrHuang.com www.electrochem.net www.DrHuang.com www.electroanal.com It analytically and digitally simulates virtually any mechanism 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 also simulates effects of charge current, resistance, noise, electrolyte, stripping time, stripping potential, pH, 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. polar43.zip is 1589KB, including VB6 runtime dll and ocx and setup. polar43a.zip is 146 KB, without VB runtime dll and ocx and setup. New features: 1. effect of any electron number. 2. pH effect. 3. new reaction, e.g. 2A+2H+4e=3B and more. Users of versions 4.1+ may get free upgrade. *********************************************************** * Dr Weiguang Huang, BS, MS, PhD, MACS * * 124 Eastern Ave, Kingsford, Sydney, NSW 2032, Australia * * Phone: 02 96620516, 0413 008 019, 0425212734, 0283002734* * email: DrHuang@DrHuang.com, DrHuang@mail.com * * http://www.DrHuang.com, www.DoctorHuang.com * * SymbMath For Java - online math * *********************************************************** From chemistry-request@server.ccl.net Sun Feb 18 22:56:42 2001 Received: from melpop01.goconnect.net ([202.92.76.50]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1J3ufw29299 for ; Sun, 18 Feb 2001 22:56:41 -0500 Received: from pentium466 ([202.92.72.127]) by melpop01.goconnect.net (Netscape Messaging Server 4.15) with ESMTP id G8ZK7N00.431 for ; Mon, 19 Feb 2001 14:54:59 +1100 Message-ID: <005301c09a30$51505220$0100a8c0@pentium466> Reply-To: "DrHuang.com" From: "DrHuang.com" To: Subject: Fw: I upload electrochemistry software polar34.zip and polar34a.zip to ccl.net Date: Mon, 19 Feb 2001 14:56:25 +1000 Organization: DrHuang.com MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Files names on Subject should be polar43.zip and polar43a.zip, instead of polar34.zip and polar34a.zip. Sorry. ----- Original Message ----- From: "DrHuang.com" To: Sent: Monday, February 19, 2001 2:40 PM Subject: I upload electrochemistry software polar34.zip and polar34a.zip to ccl.net Polar 4.3 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 Fax: 61 2 93138266 mailto:polar@electroanal.com, polar@DrHuang.com www.electrochem.net www.DrHuang.com www.electroanal.com It analytically and digitally simulates virtually any mechanism 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 also simulates effects of charge current, resistance, noise, electrolyte, stripping time, stripping potential, pH, 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. polar43.zip is 1589KB, including VB6 runtime dll and ocx and setup. polar43a.zip is 146 KB, without VB runtime dll and ocx and setup. New features: 1. effect of any electron number. 2. pH effect. 3. new reaction, e.g. 2A+2H+4e=3B and more. Users of versions 4.1+ may get free upgrade. *********************************************************** * Dr Weiguang Huang, BS, MS, PhD, MACS * * 124 Eastern Ave, Kingsford, Sydney, NSW 2032, Australia * * Phone: 02 96620516, 0413 008 019, 0425212734, 0283002734* * email: DrHuang@DrHuang.com, DrHuang@mail.com * * http://www.DrHuang.com, www.DoctorHuang.com * * SymbMath For Java - online math * ***********************************************************