From chemistry-request@ccl.net Fri Jan 16 10:00:46 2004 Received: from plounts.uits.indiana.edu (plounts.uits.indiana.edu [129.79.1.73]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0GF0ic1007763 for ; Fri, 16 Jan 2004 10:00:44 -0500 Received: from grapeape.uits.iupui.edu (grapeape.uits.iupui.edu [134.68.220.203]) by plounts.uits.indiana.edu (8.12.10/8.12.10/IUPO) with ESMTP id i0GF1UTY019240 for ; Fri, 16 Jan 2004 10:01:30 -0500 (EST) Received: from iupui.edu ([134.68.57.154]) by grapeape.uits.iupui.edu (8.12.10/8.12.10/IUPO) with ESMTP id i0GF1VdX016470 for ; Fri, 16 Jan 2004 10:01:31 -0500 (EST) Message-ID: <4007FCD6.2040101.-at-.iupui.edu> Date: Fri, 16 Jan 2004 10:01:42 -0500 From: "Q.Z." User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry.-at-.ccl.net Subject: CCL: calculate relative hydrophobicity Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi All, I wonder anyone knows a free program to calculate the relative hydrophobicity of a ligand binding pocket in proteins. Thanks. Q.Z. From chemistry-request@ccl.net Fri Jan 16 11:32:43 2004 Received: from mailhost3.tudelft.nl (mailhost3.tudelft.nl [130.161.180.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0GGWgc1010647 for ; Fri, 16 Jan 2004 11:32:42 -0500 Received: from 127.0.0.1 (localhost [127.0.0.1]) by rav.antivirus (Postfix) with SMTP id 8F96316AA4 for ; Fri, 16 Jan 2004 17:33:30 +0100 (MET) Received: from mail.dct.tudelft.nl (tnw-dct1.dct.tudelft.nl [130.161.196.201]) by mailhost3.tudelft.nl (Postfix) with ESMTP id 4C39A16FC8 for ; Fri, 16 Jan 2004 17:33:30 +0100 (MET) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); 16 Jan 04 17:33:30 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); 16 Jan 04 17:33:28 +0200 From: "Stefan Bromley" Organization: Delft University of Technology (TNW-DCT) To: chemistry[at]ccl.net Date: Fri, 16 Jan 2004 17:33:23 +0100 MIME-Version: 1.0 Subject: CCL: Crystal prediction software Message-ID: <4008205B.1721.3435EF81@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.12a) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL, does anyone know where one can download a version of MOLPAK, DMAREL or any similar codes useful for molecular crystal structure prediction? Many thanks, Stefan Bromley ________________________________________________________ Dr Stefan T. Bromley Laboratory of Applied Organic Chemistry and Catalysis DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands Phone : + 31 1527 89418 e-mail : S.T.Bromley[at]tnw.tudelft.nl ________________________________________________________ From chemistry-request@ccl.net Fri Jan 16 10:17:44 2004 Received: from chemiome.chm.unipg.it (chemiome.chm.unipg.it [141.250.9.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0GFHhc1008380 for ; Fri, 16 Jan 2004 10:17:43 -0500 Received: from chemiome.chm.unipg.it (chemoplus [192.168.9.45]) by chemiome.chm.unipg.it (Postfix) with ESMTP id C877C2B120; Fri, 16 Jan 2004 16:18:33 +0100 (CET) Message-ID: <40080159.5000505~at~chemiome.chm.unipg.it> Date: Fri, 16 Jan 2004 16:20:57 +0100 From: Gabriele Cruciani User-Agent: Mozilla/5.0 (X11; U; IRIX IP32; en-US; rv:1.3b) Gecko/20030212 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Q.Z." Cc: chemistry~at~ccl.net Subject: calculate relative hydrophobicity References: <4007FCD6.2040101~at~iupui.edu> In-Reply-To: <4007FCD6.2040101~at~iupui.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi you can easily do it using the hydrophobic probe in GRID force field (free from www.moldiscovery.com). For precise numerical quantification of the regions, VolSurf can be used, from the same site. Enjoy Gabriele Cruciani From chemistry-request@ccl.net Fri Jan 16 10:51:46 2004 Received: from mail.gmx.net (pop.gmx.net [213.165.64.20]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i0GFpfc1009473 for ; Fri, 16 Jan 2004 10:51:42 -0500 Received: (qmail 23708 invoked by uid 0); 16 Jan 2004 15:52:26 -0000 Received: from 202.184.17.249 by www53.gmx.net with HTTP; Fri, 16 Jan 2004 16:52:17 +0100 (MET) Date: Fri, 16 Jan 2004 16:52:17 +0100 (MET) From: "Bimo Ario Tejo" To: chemistry~at~ccl.net MIME-Version: 1.0 Subject: residue cross correlation X-Priority: 3 (Normal) X-Authenticated: #19451724 Message-ID: <27031.1074268337~at~www53.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I'm just wondering does anyone have a program to calculate residue cross-correlation (DCCM) of MD trajectories based on vectors (origin at mean atom position during simulation)? I need such a program that able to read any trajectories regardless what program used (CHARMM, Amber, Gromacs, etc.)... Thank you and best regards, Bimo -- +++ GMX - die erste Adresse f|r Mail, Message, More +++ Bis 31.1.: TopMail + Digicam f|r nur 29 EUR http://www.gmx.net/topmail From chemistry-request@ccl.net Thu Jan 15 22:42:41 2004 Received: from gip2.u-picardie.fr (gip2.u-picardie.fr [193.49.184.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0G3gec1019674 for ; Thu, 15 Jan 2004 22:42:41 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id E263D9D79; Fri, 16 Jan 2004 04:43:26 +0100 (CET) To: chemistry|at|ccl.net Subject: CHELPG in GAMESS Message-ID: <1074224606.40075dded24e9|at|webmail.u-picardie.fr> Date: Fri, 16 Jan 2004 04:43:26 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, I am trying to use CHELPG in GAMESS to get electrostatic potential. In the GAMESS doc., it is written: "CHELPG: to use a modified version of the CHELPG algorithm, which produces a symmetric grid of points for a symmetric molecule" - Does it mean that the CHELPG algorithm in GAMESS is different from the published one in Breneman & Wiberg, J Comput Chem 1990, 11, 361-373 ? - If yes, why this algo. has been modified in GAMESS and/or is there a way to use the original one in GAMESS ? Thanks, regards, Francois From chemistry-request@ccl.net Fri Jan 16 13:45:11 2004 Received: from smtp2.server.rpi.edu (smtp2.server.rpi.edu [128.113.2.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0GIjAc1015215 for ; Fri, 16 Jan 2004 13:45:10 -0500 Received: from rpi.edu (scabbers-26.dynamic2.rpi.edu [128.113.134.141]) by smtp2.server.rpi.edu (8.12.8/8.12.8) with ESMTP id i0GIjwO1032554; Fri, 16 Jan 2004 13:45:58 -0500 Message-ID: <4008312D.E53D8D2A~at~rpi.edu> Date: Fri, 16 Jan 2004 13:45:01 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: FyD CC: chemistry~at~ccl.net Subject: Re: CCL:CHELPG in GAMESS References: <1074224606.40075dded24e9~at~webmail.u-picardie.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Francois, I'm not familiar with the specific CHELPG modifications made for GAMESS, but one issue with the original CHELPG routine was the possibility of computing atomic charges that do not coincide with molecular symmetry. In the original implementation, no special attention was paid to assuring that the 3D grid of sampled points was symmetrically distributed with respect to molecular symmetry elements. The effect can result in unequal ESP charges being computed for symmetrically-related atoms. This is not always a problem - In fact, it was found that for small molecules using dense grids, (0.2 au or so), this was a minor effect. In practical applications, this can raise an issue. The variation can be large or small, depending upon the complexity of the electrostatic field and the sparsity of the sampling grid. Cheers, Curt Breneman RPI Chemistry FyD wrote: > Dear All, > > I am trying to use CHELPG in GAMESS to get electrostatic potential. In the > GAMESS doc., it is written: > "CHELPG: to use a modified version of the CHELPG algorithm, which produces a > symmetric grid of points for a symmetric molecule" > > - Does it mean that the CHELPG algorithm in GAMESS is different from the > published one in Breneman & Wiberg, J Comput Chem 1990, 11, 361-373 ? > - If yes, why this algo. has been modified in GAMESS and/or is there a way to use > the original one in GAMESS ? > > Thanks, regards, Francois > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY~at~ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST~at~ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow~at~nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+