From chemistry-request@server.ccl.net Mon Mar 10 17:27:46 2003 Received: from mxout5.cac.washington.edu ([140.142.32.135]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2AMRkq03210 for ; Mon, 10 Mar 2003 17:27:46 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout5.cac.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with ESMTP id h2AMRiEk021366; Mon, 10 Mar 2003 14:27:45 -0800 Received: from DGVR6B21 ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW03.03/8.12.1+UW02.12) with SMTP id h2AMRiwZ016287; Mon, 10 Mar 2003 14:27:44 -0800 Message-ID: <011701c2e754$48fcee80$74805f80@DGVR6B21> From: "Carsten Detering" To: Cc: Subject: NCI diversity set Date: Mon, 10 Mar 2003 23:27:50 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0114_01C2E75C.AAB9B560" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_0114_01C2E75C.AAB9B560 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi again, Did somebody work already with the recently released NCI-diversity Set = for AutoDock (to be found on the AutoDock web site)? How are the = rotatable bonds treated in this approach?? Of course, it is impossible = to edit 2000 files regarding rotatable bonds, let alone the treatment of = the hydrogen rotors -OH, -NH2 etc. Is this to be neglected until a = promising molecule is found and then redocked with the correct number?? Thanks for helpful suggestions/comments. Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Fon 206-543-5081 Fax 206-865-8665 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------=_NextPart_000_0114_01C2E75C.AAB9B560 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi again,

Did somebody work already with the = recently=20 released NCI-diversity Set for AutoDock (to be found on the AutoDock web = site)?=20 How are the rotatable bonds treated = in this=20 approach?? Of course, it is impossible to edit 2000 files = regarding=20 rotatable bonds, let alone the treatment of the hydrogen rotors -OH, = -NH2 etc.=20 Is this to be neglected until a promising molecule is found and = then=20 redocked with the correct number??

Thanks for helpful=20 suggestions/comments.

Carsten

~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten = Detering,=20 Ph.D.
University of Washington
Seattle, WA 98195
Fon=20 206-543-5081
Fax=20 206-865-8665
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

------=_NextPart_000_0114_01C2E75C.AAB9B560-- From chemistry-request@server.ccl.net Tue Mar 11 01:47:25 2003 Received: from mx3.ust.hk ([143.89.13.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2B6lOq11550 for ; Tue, 11 Mar 2003 01:47:24 -0500 Received: from ust.hk (sqmail4.ust.hk [143.89.15.14]) by mx3.ust.hk (8.12.8/8.12.8) with SMTP id h2B6lKOc044312 for ; Tue, 11 Mar 2003 14:47:21 +0800 (HKT) Received: from 143.89.53.94 (SquirrelMail authenticated user chgy) by sqmail.ust.hk with HTTP; Tue, 11 Mar 2003 14:47:21 +0800 (HKT) Message-ID: <1415.143.89.53.94.1047365241.squirrel@sqmail.ust.hk> Date: Tue, 11 Mar 2003 14:47:21 +0800 (HKT) Subject: Gibbs free energy From: "GAO Yi" To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.8) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CClers, I'm now calculating the gibbs energy via Gaussian98. I wonder whether I can use the FREQ keyword to get the gibbs corrections for the non-local minimum and whether these results are correct to represent the points of the Gibbs free energy surface. Gao Yi From chemistry-request@server.ccl.net Tue Mar 11 11:27:49 2003 Received: from dobit2.rug.ac.be ([157.193.42.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2BGRnq05711 for ; Tue, 11 Mar 2003 11:27:49 -0500 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by dobit2.rug.ac.be (8.12.8/8.12.8) with ESMTP id h2BGRnkn011026 for ; Tue, 11 Mar 2003 17:27:49 +0100 (MET) Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by allserv.rug.ac.be (8.12.8/8.12.8) with ESMTP id h2BGRm5e021053 for ; Tue, 11 Mar 2003 17:27:48 +0100 (MET) Received: from inchem34 (inchem34.rug.ac.be [157.193.91.54]) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) with SMTP id RAA06504 for ; Tue, 11 Mar 2003 17:29:51 +0100 (NFT) Message-Id: <4.1.20030311172903.00a24858@157.193.91.12> X-Sender: patrick@157.193.91.12 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Tue, 11 Mar 2003 17:31:41 +0100 To: chemistry@ccl.net From: Patrick Bultinck Subject: Molecular alignment In-Reply-To: <200211221436.gAMEa1q28876@socrates-a.ucl.ac.uk> References: <4.1.20021122135914.02aac950@127.0.0.1> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear, I am developing a new technique for molecular alignment, based on quantum chemistry. I would like to know more about the more traditional methods to produce the translation and rotation of molecules as a whole. More precisely, I am looking for methods that do NOT - involve Euler's angles (parameters) - depend on first aligning mass centres. Surely, there must have been published some other affine techniques, and you would help a lot if you could point in some good direction ! Thanks, Patrick Bultinck Ghent Quantum Chemistry Group Ghent University Belgium From chemistry-request@server.ccl.net Tue Mar 11 12:23:48 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2BHNmq07720 for ; Tue, 11 Mar 2003 12:23:48 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.8/jtpda-5.4) with SMTP id h2BHNlZC011086 for ; Tue, 11 Mar 2003 18:23:47 +0100 (CET) Date: Tue, 11 Mar 2003 18:23:47 +0100 Message-Id: <03031118234701@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: CHEMISTRY@ccl.net Subject: CCL:Re: Molecular alignment X-VMS-To: SMTP%"CHEMISTRY@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr To: CHEMISTRY@ccl.net Subject: CCL:Re: Molecular alignment A traditional non parametric method is used by CSR: goto http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR and look at the reference in the documentation. Since it is a purely geometric method, the mean points of the common 3D motifs are aligned (but NOT those of the whole molecules). This is a consequence of the optimality of the translation, for the rms criterion, applied to the pair of common 3D motifs. Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html >Dear, > >I am developing a new technique for molecular alignment, based on quantum >chemistry. I would like to know more about the more traditional methods to >produce the translation and rotation of molecules as a whole. More >precisely, I am looking for methods that do NOT >- involve Euler's angles (parameters) >- depend on first aligning mass centres. > >Surely, there must have been published some other affine techniques, and >you would help a lot if you could point in some good direction ! > >Thanks, > >Patrick Bultinck >Ghent Quantum Chemistry Group >Ghent University >Belgium From jkl@ccl.net Mon Mar 10 14:48:05 2003 -0500 Return-Path: Date: Mon, 10 Mar 2003 14:48:04 -0500 (EST) From: Yong Liang Yang To: chemistry@ccl.et Subject: .cpd file and .mmod file Message-ID: hello,CCL users: Does anybody know how to convert .cpd file (output file > from Catalyst) to .mmod file(Macromodel input file)? Or .cpd file can be read by Macromodel program? Great thanks in advances! Yongliang Yang Stony Brook 11794 From chemistry-request@server.ccl.net Tue Mar 11 14:57:57 2003 Received: from facepe.dqf.ufpe.br ([150.161.5.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2BJvtq13887 for ; Tue, 11 Mar 2003 14:57:56 -0500 Received: from dqf.ufpe.br ([150.161.5.90]) by facepe.dqf.ufpe.br (8.12.6/8.12.6) with ESMTP id h2BHaJ2G069622 for ; Tue, 11 Mar 2003 14:36:19 -0300 (BRT) (envelope-from sidney@dqf.ufpe.br) Message-ID: <3E6E4181.9020106@dqf.ufpe.br> Date: Tue, 11 Mar 2003 17:05:21 -0300 From: Sidney Ramos de Santana User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List Subject: ECPs in the dalton 1.2 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCL Users, Would I know if can I use ECPs in the dalton1.2 ? If your answer was "yes !" Please, could someone send me a example for this. Best Regards, Sidney Ramos Graduate Program of Material Science CCEN - UFPE From chemistry-request@server.ccl.net Tue Mar 11 17:50:20 2003 Received: from sherman.che.utexas.edu ([128.83.162.80]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2BMoKr20900 for ; Tue, 11 Mar 2003 17:50:20 -0500 Received: from einstein.che.utexas.edu (einstein.che.utexas.edu [128.83.162.4]) by sherman.che.utexas.edu (8.10.1/8.10.1) with ESMTP id h2BMoKN18444 for ; Tue, 11 Mar 2003 16:50:20 -0600 (CST) Received: from localhost (wang@localhost) by einstein.che.utexas.edu (8.11.6/8.11.6) with ESMTP id h2BMk8009109 for ; Wed, 12 Mar 2003 04:46:08 +0600 X-Authentication-Warning: einstein.che.utexas.edu: wang owned process doing -bs Date: Wed, 12 Mar 2003 04:46:08 +0600 (GMT-6) From: Yun Wang To: chemistry@ccl.net Subject: How to set fixed basis set with polarization in Gamess In-Reply-To: <27022003173504-jkl-resent@janice.schrodinger.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Colleages, I try to calculate the systems with fixed basis sets with d polarization. The Gamess is used. Could you give me an example? With my best wishes! Andrew From chemistry-request@server.ccl.net Tue Mar 11 20:51:45 2003 Received: from adenine.cgl.ucsf.edu ([169.230.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2C1pjr26398 for ; Tue, 11 Mar 2003 20:51:45 -0500 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.8/8.12.8/GSC1.16) with ESMTP id h2C1pkVO638609 for ; Tue, 11 Mar 2003 17:51:46 -0800 (PST) Date: Tue, 11 Mar 2003 17:51:46 -0800 (PST) From: Pradipta Bandyopadhyay To: chemistry@ccl.net Subject: non-linear fitting with MINPACK!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am using the routine lmdif.f from MINPACK for non-linear optimization. It works fine for a subset of my data - but doesn't seem to work with the larger set of data. Apparently it is trapped in some local minimum (typical of any non-linear optimization). Has anybody used it for ~ half million data points (3d grid - X . Y . Z ~ half million) successfully? Any help would be appreciated. Pradipta