From chemistry-request@ccl.net Wed Jan 14 10:43:48 2004 Received: from klingon.uab.es (klingon.uab.es [158.109.14.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0EFhlc1029119 for ; Wed, 14 Jan 2004 10:43:47 -0500 Received: from obelix.qf.uab.es ([158.109.14.83] helo=klingon.uab.es) by klingon.uab.es with esmtp (Exim 3.36 #1 (Debian)) id 1Agmwh-0002p0-00 for ; Wed, 14 Jan 2004 16:28:39 +0100 Message-ID: <400562FB.10107(at)klingon.uab.es> Date: Wed, 14 Jan 2004 16:40:43 +0100 From: Olivier Reply-To: olivier(at)klingon.uab.es User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.0) Gecko/20020623 Debian/1.0.0-0.woody.1 X-Accept-Language: en MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: tinker and Xtalmin 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 Hello, I would like to compute the structure of a monolayer of organic molecules using the xtalmin program of the Tinker package. Does anybody ever experienced this kind of calculation with Tinker ? Thanks Olivier From chemistry-request@ccl.net Wed Jan 14 07:55:57 2004 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0ECtuc1022773 for ; Wed, 14 Jan 2004 07:55:56 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AgkZX-000NHmC; Wed, 14 Jan 2004 13:56 +0100 Message-ID: <40043528.5070700(at)chem.vu.nl> Date: Tue, 13 Jan 2004 19:12:56 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: sa.cosco(at)virgilio.it CC: chemistry(at)ccl.net Subject: Re: CCL:MD after Autodock References: <4002B18800001981(at)ims1b.cp.tin.it> In-Reply-To: <4002B18800001981(at)ims1b.cp.tin.it> 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 sa.cosco(at)virgilio.it wrote: > Dear CCL > I performed a partial flexible docking analysis of some ligands, using Autodock, > on a receptor modelled by means of homology building .The complexes obtained > were geometrically optimized and energetically minimized. Is it really necessary > to perform a MD simulation after the docking and the minimization? Any suggestion > will be appreciated From doing the MD simulations you can learn several things: - flexibility in a certain binding mode, i.e. how much can the ligand move - stability of the protein in presence of the ligand, which can be especially interesting in case of a homology model - a 'second opinion' on the binding mode found by AutoDock by another program, i.c. the MD package and associated forcefield. Having said that, no, it is not really necessary... But I'd strongly advise for it ;-) -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra(at)chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Wed Jan 14 08:19:59 2004 Received: from mail2.cc.huji.ac.il (real-outmail.cc.huji.ac.il [132.64.1.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0EDJwc1023652 for ; Wed, 14 Jan 2004 08:19:59 -0500 Received: by mail2.cc.huji.ac.il (Postfix, from userid 31998) id B98AC3FE35; Wed, 14 Jan 2004 15:20:34 +0200 (IST) Received: from amiram12.md.huji.ac.il (amiram12.md.huji.ac.il [132.64.165.247]) by mail2.cc.huji.ac.il (Postfix) with ESMTP id A53743FE1A for ; Wed, 14 Jan 2004 15:20:03 +0200 (IST) Content-Type: text/plain; charset="iso-8859-1" From: Tal Lavy Subject: Search for small molecules Date: Wed, 14 Jan 2004 15:06:51 +0200 User-Agent: KMail/1.4.3 To: CHEMISTRY-.at.-ccl.net MIME-Version: 1.0 Message-Id: <200401141506.51033.tallavy-.at.-md.huji.ac.il> X-Spam-Level: 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i0EDK0c1023661 Dear CCL'ers I'm interested in small molecules (not peptides) which are flexible (with 6 or more rotatable bonds) and are known to have a dominant conformation in gas or liquid phase. If anyone knows of or has worked with this kind of molecules, I'll be happy to know about it, Thank you in advance, Tal =========================================================== Tal Lavy, Molecular Modeling and Drug Design Department of Medicinal Chemistry and Natural Products School of Pharmacy Hebrew University of Jerusalem ISRAEL Phone: 972-2-6757026 Fax: 972-2-6758925 e-mail: tallavy-.at.-md.huji.ac.il http://www.md.huji.ac.il/models ============================================================ From chemistry-request@ccl.net Wed Jan 14 07:15:11 2004 Received: from mailhub1.shef.ac.uk (mailhub1.shef.ac.uk [143.167.1.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0ECFAc1021091 for ; Wed, 14 Jan 2004 07:15:10 -0500 Received: from stoat.shef.ac.uk ([143.167.2.1]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #4) id 1Agjw6-00064X-00 for chemistry[at]ccl.net; Wed, 14 Jan 2004 12:15:50 +0000 Received: from li1vg (helo=localhost) by stoat.shef.ac.uk with local-esmtp (Exim 3.14 #2) id 1Agjw5-0002Jb-00 for chemistry[at]ccl.net; Wed, 14 Jan 2004 12:15:49 +0000 Date: Wed, 14 Jan 2004 12:15:49 +0000 (GMT) From: Val Gillet X-Sender: li1vg@stoat To: chemistry[at]ccl.net Subject: CCL: Sheffield Chemoinformatics Conf. April 2004 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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 Registration for the 3rd Joint Sheffield Conference on Chemoinformatics is now open. If you wish to attend, please visit the web site and fill out your details as directed (cisrg.shef.ac.uk/shef2004). Please note that registration includes accommodation at Tapton Hall and meals as specified in the Programme. The Programme of oral presentations and abstracts are also now available at the website. Bursaries are available for graduate students who will present a poster at the conference. The bursaries are being awarded by the Chemical Computing Group, the Molecular Graphics and Modelling Society and the Chemical Structure Association Trust and will include conference registration, accommodation and a contribution towards travel expenses. Applications, as detailed on the web site, should be emailed to Val Gillet (v.gillet[at]sheffield.ac.uk) by February 20th. --------------------------------------------------------------- Val Gillet Dept. Information Studies, University of Sheffield, Regent Court, 211 Portobello Street, Sheffield S1 4DP. Phone: +44 (0) 114 2222 652 Fax: +44 (0) 114 2780 300 --------------------------------------------------------------- From chemistry-request@ccl.net Wed Jan 14 17:07:23 2004 Received: from smtp3.lucky.net (smtp3.lucky.net [62.244.55.204]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0EM7Fc1008383 for ; Wed, 14 Jan 2004 17:07:18 -0500 Received: from smtp.lucky.net (smtp1.lucky.net [193.193.193.117]) by smtp3.lucky.net (postfix-1.1.5) with ESMTP id 8D0AA36ECD for ; Thu, 15 Jan 2004 00:07:53 +0200 (EET) Received: from kozlik.carrier.kiev.ua (smmsp$at$kozlik.carrier.kiev.ua [193.193.193.111]) by smtp.lucky.net with ESMTP id i1EM7G9Q040940 for ; Thu, 15 Jan 2004 00:07:22 +0200 (EET) (envelope-from vkhavr$at$compchem.kiev.ua) Received: (from uucp@localhost) by kozlik.carrier.kiev.ua with UUCP id i1EM7D0M097510 for CHEMISTRY$at$ccl.net; Thu, 15 Jan 2004 00:07:13 +0200 (EET) (envelope-from vkhavr$at$compchem.kiev.ua) Received: from compchua.UUCP (uucp@localhost) by kozlik.carrier.kiev.ua (rmail mypid=97509 childpid=97510) with UUCP; Wed, 14 Jan 2004 22:07:13 +0000 GMT Received: from P4 (p4.compchem.kiev.ua [10.0.0.4]) by hub.compchem.kiev.ua (8.8.8/8.8.8) with SMTP id XAA32518 for ; Wed, 14 Jan 2004 23:57:11 +0200 Message-ID: <000a01c3daea$68d77920$0400000a$at$compchem.kiev.ua> From: "Vladimir Khavryutchenko" To: Subject: CCL: d-orbitals and transition metals in semiempirical methods Date: Thu, 15 Jan 2004 00:04:40 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C3DAFB.2C3875D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Verify-Sender: verified X-Spam-Status: No, hits=0.0 required=7.0 tests=HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C3DAFB.2C3875D0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: quoted-printable Dear CCL'ers I am interested in d-orbitals and transition metals in the modern = semiempirical quantum chemical methods and their realizations. If anyone = knows of the good articles, reviews and so on, please, inform me and, if = it is possible, send me a copy or file. We have some difficulty with = scientific journals and books last 15 years. If anyone knows of the method, introduced into MOPAC6/7 for the = transition metals? There is not parameterization for these elements, but = the parameter set is available from HyperChemT 7 from Hypercube, Inc. = The parameter's files are not marked as copyrighted. Evaluation copy of = HyperChemT 7 can compute some transition metal compounds, but there are = not any references about used method, due to Stewart's PM3 method was = designed for sp-basis only. Up to me, it means that all results, = obtained using HyperChemT 7 for transition metal compounds can not be = discussed due to unpublished and undescribed method was applied.=20 If anyone knows of the sites or other open sources for the SINDO and = MSINDO method, please, inform me too. It is a pity, that new method = developing is only for the commercial software. LINUX history is a good = example for the collective developing of the complicated software. I'll be happy to know more about this and, if these problems are = interesting, I'll post the replies. I am ready to discuss these problems = directly. Thank you in advance, Vladimir=20 VladimirKhavryutchenko=20 PhD in chemistry Computation Chemistry Group Institute for Sorbtion and Problem of Endoecology National Academy of Science of Ukraine, Kiyv UKRAINE Phone: +38(044)563-42-74 e-mail: vkhavr$at$compchem.kiev.ua ------=_NextPart_000_0007_01C3DAFB.2C3875D0 Content-Type: text/html; charset="koi8-r" Content-Transfer-Encoding: quoted-printable
Dear CCL'ers
 
I am interested in d-orbitals and = transition=20 metals in the modern semiempirical quantum chemical methods and their=20 realizations. If anyone knows of the good articles, reviews and so on, = please,=20 inform me and, if it is possible, send me a copy or file. We have some=20 difficulty with scientific journals and books last 15 years.
If = anyone knows=20 of the method, introduced into MOPAC6/7 for the transition metals? There = is not=20 parameterization for these elements, but the parameter set is available = from=20 HyperChem™ 7 from Hypercube, Inc. The parameter’s files are = not marked as=20 copyrighted. Evaluation copy of HyperChem™ 7 can compute some = transition metal=20 compounds, but there are not any references about used method, due to = Stewart’s=20 PM3 method was designed for sp-basis only. Up to me, it means that all = results,=20 obtained using HyperChem™ 7 for transition metal compounds can not = be discussed=20 due to unpublished and undescribed method was applied.
 
If anyone knows of the sites or = other open=20 sources for the SINDO and MSINDO method, please, inform me too. It is a = pity,=20 that new method developing is only for the commercial software. LINUX = history is=20 a good example for the collective developing of the complicated=20 software.
I'll be happy to know more about this and, if these = problems are=20 interesting, I’ll post the replies. I am ready to discuss these = problems=20 directly.
 
 
 
Thank you in advance,
Vladimir =
 

VladimirKhavryutchenko =
PhD in=20 chemistry
Computation Chemistry Group
Institute for Sorbtion and = Problem=20 of Endoecology
National Academy of Science of Ukraine,=20 Kiyv
UKRAINE
Phone: +38(044)563-42-74
e-mail: vkhavr$at$compchem.kiev.ua
------=_NextPart_000_0007_01C3DAFB.2C3875D0-- From chemistry-request@ccl.net Wed Jan 14 16:57:28 2004 Received: from f04n07.cac.psu.edu (f04s07.cac.psu.edu [128.118.141.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0ELvRc1008063 for ; Wed, 14 Jan 2004 16:57:27 -0500 Received: from [128.118.199.40] (ra.chem.psu.edu [128.118.199.40]) by f04n07.cac.psu.edu (8.9.3p2.1/8.9.3) with ESMTP id QAA10016 for ; Wed, 14 Jan 2004 16:58:08 -0500 Subject: increasing optimization cycles in Mopac From: Rajarshi Guha Reply-To: rxg218!at!psu.edu To: chemistry!at!ccl.net Content-Type: text/plain Message-Id: <1074117288.16715.10.camel!at!ra.chem.psu.edu> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.5 (1.4.5-7) Date: Wed, 14 Jan 2004 16:54:48 -0500 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.9 required=7.0 tests=FROM_ENDS_IN_NUMS, LINES_OF_YELLING,MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I'm trying to do a geometry optimization with Mopac 7.04. The keywords I have specified are pm3 t=999999.9 ef hess=1 mmok let gnorm= However the cacluation does not end properly and I get the error: EXCESS NUMBER OF OPTIMIZATION CYCLES Looking through the Mopac manual I dont see anyway to increase the number of optimization cycles. Does anybody know how can I increase the number of cycles so that I can achieve the SCF field? Thanks, ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Accuracy, n.: The vice of being right