From chemistry-request@server.ccl.net Tue Oct 16 03:20:55 2001 Received: from lancelot.imb-jena.de ([192.124.248.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9G7KsB28174 for ; Tue, 16 Oct 2001 03:20:54 -0400 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id JAA12470 for chemistry@ccl.net; Tue, 16 Oct 2001 09:20:54 +0200 (CEST) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10110160920.ZM206492@lancelot.imb-jena.de> Date: Tue, 16 Oct 2001 09:20:54 +0000 In-Reply-To: Eugene Leitl "CCL:FYI:Call-For-Participation: 2nd Workshop on Linux Cluster for SuperComputing (fwd)" (Oct 11, 5:48pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Subject: ccalculation of nmr order parameters Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii dear CCLers: i shall be very grateful for any pointer or reference to ways of calculating (better would be an existing implementation of such a method) generalized squared order parameters (S^2, from nmr relaxation measurements) on the basis of mean atomic fluctuations derived from a several ns md trajectory at constant temperature. many thanks in advance for your attention and feedback. best regards felipe -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Tue Oct 16 04:36:54 2001 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9G8asB29975 for ; Tue, 16 Oct 2001 04:36:54 -0400 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id KAA00229 for ; Tue, 16 Oct 2001 10:37:21 +0200 (MEST) Message-ID: <3BCBF25E.F4BC2C61@fy.chalmers.se> Date: Tue, 16 Oct 2001 10:39:59 +0200 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: Glass transition temperature Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleagues, does anyone out there know of the applicability of computed torsional barriers (by SE, HF, MP2 methods etc) about single bonds as a way to predict glass transition temperatures (absolute or relative) for simple polymers? The computations of course on oligomers. Will summarize to the list. all the best /Patrik -- Dr. Patrik Johansson Scientist Materials Physics Chalmers University of Technology 412 96 Goteborg SWEDEN patrikj@fy.chalmers.se http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Tue Oct 16 10:49:04 2001 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9GEmqB05021 for ; Tue, 16 Oct 2001 10:49:04 -0400 Received: from attglobal.net (slip-32-101-104-243.in.us.prserv.net[32.101.104.243]) by prserv.net (out4) with SMTP id <20011016144851204036so6be>; Tue, 16 Oct 2001 14:48:51 +0000 Message-ID: <3BCBF67F.5FEFFCCA@attglobal.net> Date: Tue, 16 Oct 2001 09:57:35 +0100 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.51 [en]C-CCK-MCD (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Corel Linux Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello.. Is there a Corel Linux user or two out there that could assist me in straightening out a networking issue [so I can offload a lot of DFT computation results and then install Red Hat Linux?] Or.. can I just install RH Linux on top of Corel Linux without damaging/endangering the DFT results I want to save? Thanks! John McKelvey From chemistry-request@server.ccl.net Mon Oct 15 23:48:14 2001 Received: from web20704.mail.yahoo.com ([216.136.226.177]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9G3mDB24983 for ; Mon, 15 Oct 2001 23:48:13 -0400 Message-ID: <20011016034813.51668.qmail@web20704.mail.yahoo.com> Received: from [64.165.229.61] by web20704.mail.yahoo.com via HTTP; Mon, 15 Oct 2001 20:48:13 PDT Date: Mon, 15 Oct 2001 20:48:13 -0700 (PDT) From: Masakatsu Watanabe Subject: Re: CCL:molecular dynamic: wich program? To: Mirco Meniconi , chemistry@ccl.net In-Reply-To: <001201c153cf$2b88b600$3eda623e@mircomputer> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Mirco, Check the web-site http://home.pacbell.net/masa_w. Event though the web is still in the construction, you can find the link to the book "Computational Biophysics and Biochemistry" appendix. Check the section B on the appendix, you can find the list of the popular MD packages (each one has the link). Hopefully, you can find it useful. Masa Watanabe --- Mirco Meniconi wrote: > Hi all, > I'm looking for a free program for bio-molecular > dynamics simulations, capable to run under a > multiprocessor system. > could you send me the web-addres where I can find > out this program? > thanks for yours help. ===== ========================================================= Masakatsu Watanabe, Ph.D. Wavefunction, Inc. Scientific Developer 18401 Von Karman, Suite 370 E-mail: masa@wavefun.com Irvine, CA 92612, USA Phone: 949-955-2120 FAX: 949-955-2118 Web: http://www.wavefun.com =========================================================== From chemistry-request@server.ccl.net Tue Oct 16 21:05:16 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9H15GB16327 for ; Tue, 16 Oct 2001 21:05:16 -0400 Received: from Laurence.mbi.ucla.edu (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id f9H15Fq18064 for ; Tue, 16 Oct 2001 18:05:15 -0700 (PDT) Message-Id: <5.1.0.14.2.20011016175929.0396ac48@127.0.0.1> X-Sender: lavelle/mbi.ucla.edu@127.0.0.1 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 16 Oct 2001 18:08:26 -0700 To: CCL From: Laurence Lavelle Subject: Orbital energies for 1st row transition metals. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed The following question relates to a first year chemistry course that I teach. Cr ground state is [Ar]3d^5 4s^1 What would be the ground state for Cr^-1 ? Explain the e- configuration and estimate the relative energy difference between Cr and Cr^-1. Discussion and comments welcome. Best, Laurence Lavelle From chemistry-request@server.ccl.net Tue Oct 16 21:46:27 2001 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9H1kQB17036 for ; Tue, 16 Oct 2001 21:46:26 -0400 Received: from samay (samay.ee.sc.edu [129.252.22.248]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id 481DQ8N2; Tue, 16 Oct 2001 21:41:05 -0400 Message-ID: <000b01c156ac$eecc13c0$f816fc81@ee.sc.edu> From: "derosa" To: Subject: Universal Force Field (UFF) Date: Tue, 16 Oct 2001 21:42:07 -0400 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear all: I am trying to figure out how the Universal Force Field is parameterized in Cerius2, particularly the torsion and the inversion interactions. My source is the Paper of Rappe et al J. Am. Chem. Soc. 1992 114, 10024 and the set of parameter shown in the force field UFF 1.02. According to what I understood from that paper, the torsional energy is given by E=1/2 V[1-cos(n*phi0)*cos(n*phi)] It is a little obscure for me how this parameters are defined For sp2 centers connected to another sp2 center n=2 and phi0 is 180, which is my case. so E=1/2 V [1-cos(2*phi)] My first question is how V is defined. In the mentioned paper there are two different sum rules depending on whether the center is sp2 or sp3 however only for sp3 centers V is defined as a function of a "torsional barrier factor" of each atoms which is the only parameter (I could find) in the force field. SO how is V defined (in cerius2) for sp2 centers, which is the sum rule I should use?. With respect to the inversion, Rappe et al indicates that the inversion energy is given by E=Kijkl( Co + C1 sin(Gamma)+ C2 cos(2Gamma)) However UFF, as implemented in cerius2 only offers two parameters, the inversion barrier and the equilibrium inversion angle for each atoms. How the other parameters are obtained?, is the previous formula the one that is used in cerius2?. Any clarifying comment will be much appreciated. You can send the answers directly to me at derosa@engr.sc.edu I will summarize if there is any interest. Thank you very much for your help, Pedro From chemistry-request@server.ccl.net Tue Oct 16 14:02:57 2001 Received: from eden.rutgers.edu ([165.230.180.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9GI2vB08743 for ; Tue, 16 Oct 2001 14:02:57 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by eden.rutgers.edu (Postfix) with ESMTP id E026726F7A for ; Tue, 16 Oct 2001 14:02:56 -0400 (EDT) Message-ID: <3BCC78D0.7F983BC0@eden.rutgers.edu> Date: Tue, 16 Oct 2001 14:13:36 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Water models Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Can anyone suggest a good, recent review of the various models for water (e.g.,TIP3P,etc.)? Thanks! Mary O'Connor Doctoral Candidate Rutgers University New Brunswick, NJ USA From chemistry-request@server.ccl.net Tue Oct 16 17:00:16 2001 Received: from hotmail.com ([216.33.241.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9GL0FB11946 for ; Tue, 16 Oct 2001 17:00:16 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 16 Oct 2001 14:00:10 -0700 Received: from 134.129.118.52 by lw8fd.law8.hotmail.msn.com with HTTP; Tue, 16 Oct 2001 21:00:10 GMT X-Originating-IP: [134.129.118.52] From: "xin hu" To: ngpeiling1@yahoo.com Cc: chemistry@ccl.net Subject: Re: charges needed in AutoDock3.0 Date: Tue, 16 Oct 2001 21:00:10 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 16 Oct 2001 21:00:10.0864 (UTC) FILETIME=[8B2BFF00:01C15685]

Hi, Sorry for the late reply. I donot know if you installed the ADT, the graphic interface for AutoDock. You can assigned the Gasteiger-Marsili charges on the small molecules directly using ADT, or you can compute the charge using SYBYL or HyperChem, and then convert to the lig.pdbq format using some scripts that AutoDOck provided.

There are lots of reference about AutoDock, you may check the website of AutoDOck.

Hope help.

 

Xin Hu




----------------------------------------------------------
Xin Hu
Department of Pharmaceutical Sciences
College of Pharmacy
North Dakota State University
Fargo, ND 58105
Tel: 701-231-8298(office)
701-231-4307(home)
701-231-7781(Fax)
E-mail: xin_hu@ndsu.nodak.edu
xxh0541@hotmail.com
Mail address:
13 Bison Court
Fargo, ND 58102
----------------------------------------------------------
----Original Message Follows----
From: Ng Pei Ling
To: xin hu
Subject: Re: charges needed in AutoDock3.0
Date: Fri, 12 Oct 2001 01:24:03 -0700 (PDT)
MIME-Version: 1.0
Received: from [216.136.225.54] by hotmail.com (3.2) with ESMTP id MHotMailBD8FF3C000C740043261D888E13607C40; Fri, 12 Oct 2001 01:24:32 -0700
Received: from [161.142.15.4] by web14902.mail.yahoo.com via HTTP; Fri, 12 Oct 2001 01:24:03 PDT
From ngpeiling1@yahoo.com Fri, 12 Oct 2001 01:25:46 -0700
Message-ID: <20011012082403.71006.qmail@web14902.mail.yahoo.com>
In-Reply-To:
Dear Xin Hu :
Can you help me to assign charges for small
molecule such as flavonoids ? My supervisor ask me to
do this before docking. But, I still don't know how.
Thanks if you can also send me some references for
autodock.
--- xin hu wrote:
> Hello, AutoDock user:
> I have a question about the charges of
> macromolecules used in AutoDock. Why
> it must be integral? I got the error warning with
> non-integral charges of
> protein (for some residues such as GLU the charge is
> -0.999 rather than
> -1.0), but I can still run the AutoDock and nothing
> different with the
> result. The same thing for the ion such as Mg. I
> assign an ab intio derived
> charge with +0.8e (for example) rather than +2.0, It
> is non-integral, but I
> found it is working well.
> Would someone please tell me why?
>
> Thanks for your help.
>
>
>
> Xin Hu
> Department of Pharmaceutical Sciences
> College of Pharmacy
> North Dakota State University
> Fargo, ND 58105
>
----------------------------------------------------------
>
>
>
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From chemistry-request@server.ccl.net Tue Oct 16 13:01:59 2001 Received: from mailhost.univ-orleans.fr (IDENT:root@[194.167.30.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9GH1xB07749 for ; Tue, 16 Oct 2001 13:01:59 -0400 Received: from univ-orleans.fr (aneto.univ-orleans.fr [193.49.95.24]) by mailhost.univ-orleans.fr (8.9.3/jtpda-5.3.1) with ESMTP id TAA24627 for ; Tue, 16 Oct 2001 19:01:58 +0200 Message-ID: <3BCC6A2B.5700E841@univ-orleans.fr> Date: Tue, 16 Oct 2001 19:11:08 +0200 From: nicolas baurin X-Mailer: Mozilla 4.75 [fr] (WinNT; U) X-Accept-Language: fr MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: summary : known and future drug targets: literature references Content-Type: multipart/alternative; boundary="------------7DFD91D11F9D5255E86C7D64" Content-Transfer-Encoding: 8bit --------------7DFD91D11F9D5255E86C7D64 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLer's, thanks a lot for all who reply to my question about litterature references citing the number of now known drug targets and an estimation of future drug target from genome data: i got many mail giving personal estimations and you'll find below the literature references i received. Concerning the drug trial failure, I found a web reference at http://innovation.phrma.org ("Only five in 5,000 compounds that enter preclinical testing make it to human testing. One of these five tested in people is approved"). Eric Vangrevelinghe wrote http://www.bcg.com/publications/files/genomics.pdf Drews, J. Drug discovery: A historical perspective [Review]. (Science. 287(5460):1960-1964, 2000 Mar 17). Caron et al. Chemogenomic approaches to drug discovery. (Current Opinion in Chemical Biology 2001, 5:464-470). -- Nicolas Baurin Doctorant Laboratoire de Chimiométrie - Modélisation Moléculaire Institut de Chimie Organique et Analytique, UMR 6005 http://www.univ-orleans.fr/SCIENCES/ICOA/ Université d'Orléans, BP 6759 45067 ORLEANS Cedex 2, France Tel: (33+) 2 38 49 45 77 --------------7DFD91D11F9D5255E86C7D64 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLer's,
thanks a lot for all who reply to my question about litterature references citing the number of now known drug targets and an estimation of future drug target from genome data: i got many mail giving personal estimations and you'll find below the literature references i received. Concerning the drug trial failure, I found a web reference at http://innovation.phrma.org ("Only five in 5,000 compounds that enter preclinical testing make it to human testing. One of these five tested in people is approved").

Eric Vangrevelinghe wrote
    http://www.bcg.com/publications/files/genomics.pdf

    Drews, J. Drug discovery: A historical perspective [Review]. (Science.
    287(5460):1960-1964, 2000 Mar 17).

    Caron et al. Chemogenomic approaches to drug discovery. (Current Opinion
    in Chemical Biology 2001, 5:464-470).

--
Nicolas Baurin

Doctorant
Laboratoire de Chimiométrie - Modélisation Moléculaire
Institut de Chimie Organique et Analytique, UMR 6005
http://www.univ-orleans.fr/SCIENCES/ICOA/
Université d'Orléans, BP 6759
45067 ORLEANS Cedex 2, France
Tel: (33+) 2 38 49 45 77
  --------------7DFD91D11F9D5255E86C7D64--