From chemistry-request@server.ccl.net Sat Jan 22 03:57:17 2000 Received: from linux2.ipc.pku.edu.cn (mao@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA26708 for ; Sat, 22 Jan 2000 03:57:14 -0500 Received: from localhost (mao@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id PAA13899 for ; Sat, 22 Jan 2000 15:56:04 +0800 Date: Sat, 22 Jan 2000 15:56:04 +0800 (CST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: How to place a protein molecule to a water box? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, all, I want to place a protein to a water box, which program can do this, and how to do? Thank s for any reply. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Institute of Physical Chemistry Peking University BeiJing P.R.China Tel:86-10-62756833 Fax:86-10-62751725 From chemistry-request@server.ccl.net Sat Jan 22 14:20:34 2000 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29847 for ; Sat, 22 Jan 2000 14:20:34 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id NAA19950 for ; Sat, 22 Jan 2000 13:17:23 -0500 (EST) Date: Sat, 22 Jan 2000 13:17:22 -0500 (EST) From: Iraj Daizadeh To: chemistry@ccl.net Subject: md simulations/small chunks of proteins Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Members of the CCL: Here are some questions that I have been interested in for some time; your thoughts would be appreciated. Here's the general problem: Given a alpha helix cut out from a PDB protein, run md simulations to determine the folling: 1. How can we ensure from md simulations that the alpha helix is stable in solution? We solvate the alpha helix the run md simulations for how long? how much water [10 angstrom solvation shell?]? how many time steps? how long will the calculation take? and on what machine-- Cray? etc....details--details--details! 2. References showing that results of the above calculation have been verified by experiment? References describing results of the above calculations on such small subsets of PDB data? I ( as usual ) will post a summary of your responses. Thanks, Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh From chemistry-request@server.ccl.net Sat Jan 22 15:27:24 2000 Received: from dep.chem.rug.nl (dep.chem.rug.nl [129.125.7.81]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA30107 for ; Sat, 22 Jan 2000 15:27:24 -0500 Received: from [129.125.32.62] (dialbiol02.fwn.rug.nl [129.125.32.62]) by dep.chem.rug.nl (8.9.3/8.9.3/Debian/GNU) with ESMTP id UAA02592 for ; Sat, 22 Jan 2000 20:22:10 +0100 X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <3.0.6.32.20000121165407.0095a810@pop.cee.mtu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 22 Jan 2000 20:25:00 +0200 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:polarizability >Hi all >Can anyone point me out " what's the unit of polarizability that is >obtained from frequency calculation?"? I try to find from the manual but I >didn't see they have explained about the unit. It tell you about the >polarizability tensors. I don't know how to relate to the typical unit of >polarizability such as 10^-24 cm^3. >Thanks >sompop Dear sompop, I don't know which program you use (Gaussian/ADF/HONDO/MOPAC), but there are a few common units with regards to polarizability: those regarding polarizability volumes (Atkins - Molecular Quantum Mechanics) - atomic units (i.e. Bohr^3) - Angstroms^3 -10^-24 cm^3 The second and last are equal, the first (most common !!!) is 6.748333 times ([ 1/0.52917725^3 ]) the other value. For more information I refer you again to Atkins - MQM. Best wishes, Marcel ============================================================== Marcel Swart University of Groningen Chemistry Department E-mail : m.swart@chem.rug.nl ==============================================================