From chemistry-request@server.ccl.net Mon Nov 19 02:34:31 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAJ7YMB26050 for ; Mon, 19 Nov 2001 02:34:30 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 165iwV-0004Ta-00; Mon, 19 Nov 2001 09:34:11 +0200 Received: from vejas (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id KAA03036; Mon, 19 Nov 2001 10:17:52 +0200 (GMT) Date: Sun, 18 Nov 2001 23:33:43 -0800 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <12668547205.20011118233343@vaidila.vdu.lt> To: Grzegorz Bakalarski CC: chemistry@ccl.net Subject: Re: CCL:AIM in g98 problems In-reply-To: <20011118151906.A24116@exasp.biogeo.uw.edu.pl> References: <20011118151906.A24116@exasp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I found AIM to be very capricious too. The answers about AIM in G98 are very interesting to me as well. Arturas ----------------------------> GB> Dear CCLers, GB> A collegue of mine wants to calculate bond orders in GB> guanine molecule and its modifications. She uses g98 GB> and AIM(BO,tight) keyword. She tried different methods and different GB> bases but with no success (she tried b3lyp and HF with GB> bases: STO-3G, 3-21G, 6-31G, 6-31(d), 6-31+G(d,p). GB> The only result is that she got every possible error GB> message (i.e. that some critical points are missing, GB> Newton minimizer fails etc) She also tried to use GB> some IOps (e.g IOp(6/36= ..) IOp(6/38=...) IOp(6/39=...) GB> IOp(6/55=...) but with no success. <--------------------------- From chemistry-request@server.ccl.net Mon Nov 19 06:08:13 2001 Received: from sg1503.chemie.uni-marburg.de (root@[137.248.151.215]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAJB8DB30917 for ; Mon, 19 Nov 2001 06:08:13 -0500 Received: from pc15217.chemie.uni-marburg.de (pc15217.Chemie.Uni-Marburg.DE [137.248.152.51]) by sg1503.chemie.uni-marburg.de (8.12.1/8.12.1/schn) with ESMTP id fAJB82EU024321 for ; Mon, 19 Nov 2001 12:08:03 +0100 (MET) Received: (from matthias@localhost) by pc15217.chemie.uni-marburg.de (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) id fAJB4RS32242 for chemistry@ccl.net; Mon, 19 Nov 2001 12:04:27 +0100 Date: Mon, 19 Nov 2001 12:04:27 +0100 From: Matthias Lein To: chemistry@ccl.net Subject: Re: CCL:AIM in g98 problems Message-ID: <20011119120427.A32238@chemie.uni-marburg.de> References: <20011118151906.A24116@exasp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20011118151906.A24116@exasp.biogeo.uw.edu.pl>; from grzesb@asp.biogeo.uw.edu.pl on Sun, Nov 18, 2001 at 03:19:06PM +0100 Hi, Grzegorz Bakalarski on 'CCL:AIM in g98 problems' : [AIM problems in g98] > Is there any tested set IOp's she should try? Or any other > solution? > Any help is welcome! Maybe you can use the original aimpac by the Bader group. You just have to create a .wfn file with e.g. g98 and let the aimpac suite of programs do the analysis. Cheers, Matthias. -- Matthias Lein http://www.chemie.uni-marburg.de/~matthias/anschrift.html ICQ# 47019058 PGP2.6.3iKeyID: F7B0EFD5 - Linux the choice of a GNU Generation - From chemistry-request@server.ccl.net Mon Nov 19 05:32:30 2001 Received: from exasp.biogeo.uw.edu.pl ([212.87.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAJAWTB30165 for ; Mon, 19 Nov 2001 05:32:29 -0500 Received: (from grzesb@localhost) by exasp.biogeo.uw.edu.pl (8.11.0/8.11.0) id fAJAWCx29989; Mon, 19 Nov 2001 11:32:12 +0100 Date: Mon, 19 Nov 2001 11:32:12 +0100 From: Grzegorz Bakalarski To: y tantirungrotechai Cc: chemistry@ccl.net Subject: Re: CCL:AIM in g98 problems Message-ID: <20011119113212.A29917@exasp.biogeo.uw.edu.pl> References: <20011118151906.A24116@exasp.biogeo.uw.edu.pl> <20011119080335.53261.qmail@web14704.mail.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20011119080335.53261.qmail@web14704.mail.yahoo.com>; from yt203y@yahoo.de on Mon, Nov 19, 2001 at 09:03:35AM +0100 Hello, Thanks for info! Do you think that in AIM2000 program there is easy way to calculate BOND ORDERS????? I've downloaded the program and cannot find how ... Should I integrate over some basins ??? The problem is also that my collegue is not very good in QC (and in Comp. Sci. also). She is rather biochemist, and need to know a change in bond orders upon some substitution in molecule... Best regards, gb On Mon, Nov 19, 2001 at 09:03:35AM +0100, y tantirungrotechai wrote: > The best solution is to use density(current) and > output(wfn) and punch out the .wfn file. Then use it > with Prof. Bader's aimpac or aim2000 developed by his > former coworker. Both are free and can download from > the net. > > What you need to add in, for example > *******begin********** > #p density(current) output(wfn) > > molecule specfication > > nameofoutput.wfn > > **********end *********** > > Hope this help. > Yuthana Tantirungrotechai From chemistry-request@server.ccl.net Mon Nov 19 10:18:10 2001 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAJFIAB05074 for ; Mon, 19 Nov 2001 10:18:10 -0500 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.2966); Mon, 19 Nov 2001 10:18:35 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Mon, 19 Nov 2001 10:18:00 -0500 Subject: Strain Energies From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="ISO-8859-1" X-OriginalArrivalTime: 19 Nov 2001 15:18:35.0150 (UTC) FILETIME=[74D1BAE0:01C1710D] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAJFIBB05075 Hello all, I have need of estimating the total change in strain energy from 2 starting compounds to 2 products in a hypothetical isodesmic reaction. I am aware that strain energies can be calculated by subtracting a hypothetical Hf of an "unstrained" model compound (as derived from tables such as Benson's group additivity tables) from the actual or calculated heat of formation of a compound. Unfortunately, however, I am interested in compounds for which Benson's empirical data is not (apparently) available. The question then: Is there an alternative way in which to estimate the total change in strain energy in an isodesmic reaction. Do MM calculations on an isodesmic reaction have any meaning whatsoever? Thank you for all your help! Gary W. Breton Chair and Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" From chemistry-request@server.ccl.net Mon Nov 19 19:47:35 2001 Received: from delay-3v.club-internet.fr ([194.158.96.109]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAK0lZB01682 for ; Mon, 19 Nov 2001 19:47:35 -0500 Received: from relay-3v.club-internet.fr (relay-3v.cs.clubint.net [172.16.0.114]) by delay-3v.club-internet.fr (Postfix) with ESMTP id 792626CBAA for ; Tue, 20 Nov 2001 01:22:03 +0100 (CET) Received: from sungam (nas1-11.kll.n.club-internet.fr [213.44.91.11]) by relay-3v.club-internet.fr (Postfix) with SMTP id 37E0E16C0 for ; Tue, 20 Nov 2001 01:19:59 +0100 (CET) Message-ID: <007901c17159$992a5180$0b5b2cd5@sungam> From: "Magnus" To: Subject: Appropriate docking software Date: Tue, 20 Nov 2001 01:23:22 +0100 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 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear CCLers, I am considering using a docking software to perform docking calculations between inhibitors obtained through chemical synthesis and the related protein. I have noticed that there are two "main" docking program, respectively nammed DOCK and AUTODOCK. Being no specialist at all, i would appreciate if someone could point me the merits and flaws of these two programs and which one would be the most convenient for simple flexible docking calculations. Michel Julien From chemistry-request@server.ccl.net Mon Nov 19 18:10:42 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAJNAgB30939 for ; Mon, 19 Nov 2001 18:10:42 -0500 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id fAJND0w15394 for chemistry@ccl.net; Mon, 19 Nov 2001 15:13:00 -0800 Received: from jnauss1-pc.accelrys.com (jnauss1-pc.sd.accelrys.com [172.30.51.68]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id fAJNCxX15341 for ; Mon, 19 Nov 2001 15:12:59 -0800 Message-Id: <5.1.0.14.0.20011119150207.00a45430@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 19 Nov 2001 15:04:59 -0500 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Customer Training Workshop in India Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys Inc. will be holding the "Homology-Based Protein Design Workshop" in Hyderabad and New Delhi, India in December at the offices of GVK Biosciences (http://www.gvkbio.com/). The workshop at Hyderabad will be held December 10-11. The second offering of the workshop will be December 13-14 in New Delhi. The homology workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step. Both manual and automatic methodologies will be discussed. Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII. Fees for the course are Rs10,000 commercial and Rs4,000 academic. Registration and further information may be obtained from: K.K.Bhagchandani Accelrys K.K. - India Liaison Office # 16, 3rd Cross, 13th "H" Main Doopanhalli, HAL IInd Stage, Bangalore-560008,INDIA Tele: +91 80 5216561, 5253135 Ext-33 Fax : +91 80 5216561, 5253135 Ext-32 Registration may also be made on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Please note that on 1 June, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Thank you very much. Jeffrey L. Nauss 1-858-799-5555 Chris Arzt 1-858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc. From chemistry-request@server.ccl.net Mon Nov 19 22:21:01 2001 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAK3KxB05340 for ; Mon, 19 Nov 2001 22:21:00 -0500 Received: from PC18 ([202.127.19.225]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id fAKIJKs7004974 for ; Tue, 20 Nov 2001 10:19:20 -0800 (PST) Message-Id: <200111201819.fAKIJKs7004974@mail.shcnc.AC.CN> Date: Tue, 20 Nov 2001 11:14:41 +0800 From: bxiong To: "chemistry@ccl.net" Subject: help! X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLs: I want to MD simulation the large protein, but i do not use the explicit water model, and I want to use the SA to simulate the water, how to add the SA term to AMBER FF energy function and what formula will be well suite the AMBER FF? any suggestion and reference will be helpful? thanks very much! BTW I will summarize the answer!! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office)