From chemistry-request@server.ccl.net Sun Aug 11 03:21:17 2002 Received: from hotmail.com ([64.4.23.94]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7B7LHl11979 for ; Sun, 11 Aug 2002 03:21:17 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 11 Aug 2002 00:21:12 -0700 Received: from 162.105.177.35 by lw15fd.law15.hotmail.msn.com with HTTP; Sun, 11 Aug 2002 07:21:11 GMT X-Originating-IP: [162.105.177.35] From: "Fenglei He" To: chemistry@ccl.net Subject: tools to summarize the amino residues in/around an active pocket Date: Sun, 11 Aug 2002 15:21:11 +0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 11 Aug 2002 07:21:12.0132 (UTC) FILETIME=[ABB7C840:01C24107] Hi all: I am doing some work about the amino residue propensity around the bingding pocket of some protein.Anyone can kindly tell me any software or tool available to use? For example :How to summarize all the amino residues around one pocket in the radius of 0.005 nm? Thank you He Fenglei Molecular Design Laboratory Institute of Physical Chemistry Peking University Beijing ,China _________________________________________________________________ 与联机的朋友进行交流，请使用 MSN Messenger: http://messenger.microsoft.com/cn/ From chemistry-request@server.ccl.net Sat Aug 10 20:36:25 2002 Received: from ms.cc.sunysb.edu ([129.49.2.175]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7B0aOl31745 for ; Sat, 10 Aug 2002 20:36:24 -0400 Received: from ms.cc.stonybrook.edu (ms.cc.stonybrook.edu [129.49.2.175]) by ms.cc.sunysb.edu (8.12.2/8.9.3) with SMTP id g7B0aPgX022793 for ; Sat, 10 Aug 2002 20:36:25 -0400 (EDT) Received: from ms.cc.sunysb.edu ([129.49.2.9]) by ms.cc.stonybrook.edu (NAVGW 2.5.1.16) with SMTP id M2002081020362429790 for ; Sat, 10 Aug 2002 20:36:24 -0400 Received: from ms.cc.sunysb.edu (localhost [127.0.0.1]) by ms.cc.sunysb.edu (8.12.2/8.12.2) with ESMTP id g7B0aOqQ022790 for ; Sat, 10 Aug 2002 20:36:24 -0400 (EDT) Received: from localhost (vhornak@localhost) by ms.cc.sunysb.edu (8.12.2/8.12.2/Submit) with ESMTP id g7B0aOFb022787 for ; Sat, 10 Aug 2002 20:36:24 -0400 (EDT) Date: Sat, 10 Aug 2002 20:36:24 -0400 (EDT) From: Viktor Hornak To: chemistry@ccl.net Subject: deuterated compounds in gaussian98 In-Reply-To: <005301c22c5b$8ab8ad00$a45d84d3@b159504364> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I'd like to use Gaussian98 for comparing vibration spectra of non-deuterated and deuterated form of the compound. I found "ReadIsotopes" option of "Freq" keyword and tried to use it like this (with isotope masses for all atoms after coordinate section): #P HF/6-31G* OPT FREQ(Raman,ReadIsotopes) I was wondering if someone could advise: (1) if such calculations "make sense" and (2) why I don't see anything like "H-2" (only H-1) in the output file under heading "Isotopes:". Any help is appreciated... Thanks very much, -Viktor Hornak From chemistry-request@server.ccl.net Sat Aug 10 22:15:28 2002 Received: from srv2.resnet.ohio-state.edu ([164.107.3.56]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7B2FSl04895 for ; Sat, 10 Aug 2002 22:15:28 -0400 Received: (qmail 87627 invoked by uid 1011); 11 Aug 2002 02:49:21 -0000 Received: from kiniu@mps.ohio-state.edu by srv2.resnet.ohio-state.edu with qmail-scanner-0.96 (. Clean. Processed in 0.014214 secs); 11 Aug 2002 02:49:20 -0000 Received: from rjot-84-218.resnet.ohio-state.edu (HELO kiniu) (164.107.84.218) by srv2.resnet.ohio-state.edu with SMTP; 11 Aug 2002 02:49:20 -0000 Message-ID: <002601c240dc$f29307a0$da546ba4@kiniu> From: "Kiniu WONG \(Kin-Yiu\)" To: Cc: Subject: How to get different values of the terms contributing to the HF and DFT orbital energies?? (Gaussian) Date: Sat, 10 Aug 2002 22:15:22 -0400 Organization: Physics, OSU 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear all CCLers, Both Hartree-Fock (HF) and Density Functional Theory (DFT) orbital energies are obtained by the diagonalization of the following similar equation: (T + N + C + XC) Psi = energy * Psi, where T is the kinetic energy operator, N is the nuclear attraction energy operator, C is the operator of columb repulsion energy among electrons and XC is the operator of the exchange energy among electrons. My question is: How to get the values of , , and from Gaussian? That's the expectation values of T, N, C and XC with respect to this particular orbital wavefunction Psi, e.g. Integrate[Psi N Psi] over one electron volume??? Is it true that I can obtain these values by some setting of IOps? I know that I may be able to obtain the values of and by the following methods: 1. Generate two cube files of (T Psi) and (N Psi). The keywords are "laplacian" and "potential". 2. Generate cube file of Psi. 3. Obtain and by some manipulation of these cube files by CubeMan. However, I don't know how I can get and by "Cube". Moreover, I would prefer to obtain all these expectation values analytically instead of numerically. So any suggestions? Thank you very much in advance! Wishes, Kiniu ---- Kiniu WONG (Kin-Yiu) Graduate Student Department of Physics The Ohio State University USA Primary Email: kiniu@mps.ohio-state.edu Permanent Email: kiniu@alumni.cuhk.net From chemistry-request@server.ccl.net Sun Aug 11 22:12:53 2002 Received: from ns.jfcc.or.jp ([61.123.200.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7C2Cpl23561 for ; Sun, 11 Aug 2002 22:12:52 -0400 Received: from mail1.jfcc.or.jp by ns.jfcc.or.jp () id LAA01738; Mon, 12 Aug 2002 11:11:09 +0900 (JST) Received: from yoshiya-jfcc.jfcc.or.jp by mail1.jfcc.or.jp () id g7C264t07945; Mon, 12 Aug 2002 11:06:04 +0900 (JST) Message-Id: <200208120212.AA00221@yoshiya-jfcc.jfcc.or.jp> From: Masato YOSHIYA Date: Mon, 12 Aug 2002 11:12:01 +0900 To: CHEMISTRY@ccl.net Subject: Green-Kubo formula MIME-Version: 1.0 X-Mailer: AL-Mail32 Version 1.12 Content-Type: text/plain; charset=us-ascii Dear colleagues, I am looking for a Molecular Dynamics program with which I can calculate viscosity and thermal conductivity using Green-Kubo formula. Does anybody know what program has capability to calculate them? Or, in the case I must modify the original program, what is the best program to start with? In principle, I tried to modify an existing program once and it turned out, after a modification, that modified program takes N times longer time than the original program did due to my ill-modification. It takes approximately 1000 days to be comple ted! So, I nearly gave up. Thank you for your help. Best regards, Masato YOSHIYA