From chemistry-request@server.ccl.net Mon Sep 20 05:08:36 1999 Received: from socrates.cc.uoi.gr (socrates.cc.uoi.gr [193.92.4.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA09655 for ; Mon, 20 Sep 1999 05:08:35 -0400 Received: from clibnikos (pc197.lib.uoi.gr [195.130.120.197]) by socrates.cc.uoi.gr (8.9.3/8.9.3) with SMTP id MAA2393019 for ; Mon, 20 Sep 1999 12:04:13 +0300 (EEST) Message-ID: <005601bf0346$9c57b150$c57882c3@lib.uoi.gr> From: "Nikos" To: Subject: Utility - Windows Addition to BABEL Date: Mon, 20 Sep 1999 12:00:34 +0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear all, there is a windows interface available for the well known BABEL program. It is called "Easybabel" and is located at: http://www.geocities.com/CapeCanaveral/Lab/9248/vbasic.htm It simplifies the procedure of convertion and it can be used only on windows (9*/NT) systems. As a frontend it requires the original babel. Of course it is freeware. Thank you. Nikos Kourkoumelis From chemistry-request@server.ccl.net Mon Sep 20 13:02:00 1999 Received: from ozone.umsl.edu (ozone.umsl.edu [134.124.105.185]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA12269 for ; Mon, 20 Sep 1999 13:02:00 -0400 Received: from ozone.umsl.edu (indy1.umsl.edu [134.124.105.162]) by ozone.umsl.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id AAA13029 for ; Mon, 28 Jun 1999 00:03:10 -0700 Sender: anil@ozone.umsl.edu Message-ID: <37E683CD.1C9BEC25@ozone.umsl.edu> Date: Mon, 20 Sep 1999 11:58:23 -0700 From: "Anil C. Nair" Organization: University of Missouri-St. Louis X-Mailer: Mozilla 4.07 [en] (X11; U; IRIX 6.2 IP22) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: peptide confirmational search Content-Type: text/plain; charset=x-UNICODE-2-0-UTF-7 Content-Transfer-Encoding: 7bit Dear all, I have a set 10-15 peptide molecules (with +AH4-10 aminoacid residues). I would like to generate all possible low energy conformations. I shall appreciate your suggestion regarding the best suitable software (insightII, sybyl, cerius2, spartan etc.) to do this. Also what is the best option to do the conformational search? Is it important to include solvents? Any suggestion/help in this respect will be highly appreciated. Thank you. Anil -- -------------------------------------------------------------- Anil C. Nair | Computational Chemistry Group | Phone :(314)-516-6882 Department of Chemistry | University of Missouri-St. Louis | Fax :(314)-516-5342 8001 Natural Bridge Rd. | St. Louis, MO 63121-4499, USA. | e-mail :anil@ozone.umsl.edu -------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Sep 20 16:53:56 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13592 for ; Mon, 20 Sep 1999 16:53:55 -0400 Received: from sally.schrodinger.com (sally.schrodinger.com [166.84.149.25]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id NAA11498; Mon, 20 Sep 1999 13:49:40 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.5/8.8.5) with ESMTP id QAA31551; Mon, 20 Sep 1999 16:49:08 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Mon, 20 Sep 1999 16:49:08 -0400 (EDT) From: Peter Shenkin To: "Anil C. Nair" cc: CHEMISTRY@ccl.net Subject: Re: CCL:peptide confirmational search In-Reply-To: <37E683CD.1C9BEC25@ozone.umsl.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Our MacroModel software has numerous options for conformational search and supports a variety of forcefields. Best algorithm for genreal purposes we now believe to be a mixture of LMCS (low-mode conformational search) and MCMM (which uses random torsional moves). Hope this helps, -P. On Mon, 20 Sep 1999, Anil C. Nair wrote: > Dear all, > > I have a set 10-15 peptide molecules (with +AH4-10 aminoacid residues). I > would like to generate all possible low energy conformations. I shall > appreciate your suggestion regarding the best suitable software > (insightII, sybyl, cerius2, spartan etc.) to do this. > > Also what is the best option to do the conformational search? Is it > important to include solvents? Any suggestion/help in this respect will > be highly appreciated. > > Thank you. > > Anil > > -- > -------------------------------------------------------------- > Anil C. Nair | > Computational Chemistry Group | Phone :(314)-516-6882 > Department of Chemistry | > University of Missouri-St. Louis | Fax :(314)-516-5342 > 8001 Natural Bridge Rd. | > St. Louis, MO 63121-4499, USA. | e-mail :anil@ozone.umsl.edu > -------------------------------------------------------------- > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -- ** Whether the playing field is level depends on the coordinate system. *** ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Mon Sep 20 05:20:24 1999 Received: from [194.162.211.36] ([194.162.211.36]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA09740 for ; Mon, 20 Sep 1999 05:20:24 -0400 From: Thomas.Fox@bc.boehringer-ingelheim.com Received: from gscinghub2.bikg.de by [194.162.211.36] via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 20 Sep 1999 09:15:29 UT Received: by gscinghub2.bikg.de with Internet Mail Service (5.5.2448.0) id ; Mon, 20 Sep 1999 11:15:20 +0200 Message-ID: <6183A835796ED211801A00005A4243B104F822@bc0exch7.bc.de.bic> To: CHEMISTRY@ccl.net Cc: support@gaussian.com Subject: G: PM3 ESP charges Date: Mon, 20 Sep 1999 11:14:46 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain Hi everybody - I am investigating some small molecule inhibitors of thrombin (20-30 heavy atoms) and try to extract some atomic charges with different methods and at various levels of theory with G98 Rev A7. While the Mulliken charges at all levels, and the HF-ESP charges (POP=MK, or POP=CHELP) look pretty reasonable, I have problems with the ESP charges generated by a AM1 or PM3 calculation. For some atoms I get charges of the order of +-10 ! I do know that the fitting procedure simply tries to reproduce the electrostatic potential of the wavefunction as accurately as possible and does not take into account chemical intuition or my prejudices about how big partial charges should be, and I also know the discussion of the underdetermined buried atoms, but still, 'partial' charges of this magnitude seem a little excessive to me...especially as the same molecules treated at HF level give atomic charges that very well agree with what I would have expected. So...my questions are: 1) has anybody experienced a similar behavior (which would make me much more confident that I didnt goof at some point, or that there is a bug in the new semiempirical routine) or has it been described before? 2) if my results are correct, can one rationalize why the semiempirical ESP charges are so different from the HF ones? My first guess would be that a 6-31G generated ESP is 'smoother' than a minimal basis one from the semiempirical calculations, and therefore easier to fit with atom centered monopoles, but is this really the reason? Thanks a lot, Th. -- Dr. Thomas Fox Dept. Chemical Reseach / Structural Research Boehringer Ingelheim Pharma KG 88397 Biberach/Germany Thomas.Fox@bc.boehringer-ingelheim.com