From chemistry-request@server.ccl.net Fri Jul 12 07:37:55 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6CBbsc25132 for ; Fri, 12 Jul 2002 07:37:54 -0400 Received: from wrzx34.rz.uni-wuerzburg.de (wrzx34.rz.uni-wuerzburg.de [132.187.3.34]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id NAA16347 for ; Fri, 12 Jul 2002 13:37:54 +0200 (MET DST) Received: from localhost (localhost [127.0.0.1]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 1B97C4C4A for ; Fri, 12 Jul 2002 13:37:54 +0200 (CEST) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 033F84C41 for ; Fri, 12 Jul 2002 13:37:54 +0200 (CEST) Received: from pserv.pharmazie.uni-wuerzburg.de (wpor01.pharmazie.uni-wuerzburg.de [132.187.70.201]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id E867F2D5 for ; Fri, 12 Jul 2002 13:37:53 +0200 (CEST) Received: from prgsrv2 (prgsrv2.pharmazie.uni-wuerzburg.de [132.187.74.36]) by pserv.pharmazie.uni-wuerzburg.de (8.9.3/8.9.3/uniwue-M-1.0) with ESMTP id NAA17357 for ; Fri, 12 Jul 2002 13:37:53 +0200 (MESZ) Received: from wpzn86.pharmazie.uni-wuerzburg.de ([132.187.74.86]) by prgsrv2 (MailMonitor for SMTP v1.1.0 ) ; Fri, 12 Jul 2002 13:37:52 +0200 (W. Europe Daylight Time) Message-ID: <3D2EBEB2.DF0230E1@pharmazie.uni-wuerzburg.de> Date: Fri, 12 Jul 2002 13:34:10 +0200 From: Nik X-Mailer: Mozilla 4.77 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Autodock - sort routine for docked runs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS (Rechenzentrum Universitaet Wuerzburg) Hi to all, I just started using Autodock. After eyeballing the first results, I started to wonder whether or not there is a way of resorting the docked conformations according to the different energies (e.g. Final Docked Energy, Final Intermolecular Energy etc.). I couldn't find an according tool in the share directory, therefore I wanted to ask if anybody could guide me to a link or similar where I can get something like that. I would appreciate any tool that is easily portable to Linux (e.g. fortran, c, c++, perl, etc), since it would save me the time for programming it myself ... Many thanks in advance, Nik ------------------- Nik Stiefl University of Wuerzburg Department of Pharmacy Chemometriks group Am Hubland 97074 Wuerzburg, Germany nikolaus.stiefl@mail.uni-wuerzburg.de From chemistry-request@server.ccl.net Fri Jul 12 09:34:59 2002 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6CDYxc27929 for ; Fri, 12 Jul 2002 09:34:59 -0400 Received: (qmail 31783 invoked from network); 12 Jul 2002 13:42:14 -0000 Received: from unknown (HELO test) (212.244.147.4) by mail.fqspl.com.pl with SMTP; 12 Jul 2002 13:42:14 -0000 Message-ID: <00de01c229a9$51c8c840$320a0a0a@test> From: "Victor Anisimov" To: References: <009901c2281b$46bb8e40$320a0a0a@test> Subject: Summary:Accuracy question Date: Fri, 12 Jul 2002 15:37:51 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 8bit 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 Dear CCLers, A couple of days ago I asked a question: > Based on my short investigation I could learn that HF/6-31G* is the most > popular method for electrostatic parameter optimization in Amber, Charmm, > OPLS and perhaps in other prominent force fields with the aim of the > description of molecular electrostatic potential of protein systems. > > Here I'd like to ask experts in this field. Is it the correct conclusion I > derived or perhaps other quantum-chemistry methods are more popular > for the purpose of electrostatic parameters development, e.g. databases > of ESP charges of amino acids or similar. I have got two replies. Many thanks to Prof. Jo莖 Bosco Paraiso da Silva and to Dr. E. Lewars for sharing their opinion. The short summary is that HF/6-31G* is recommended for ESP charge fitting. Nevertheless HF/3-21G is also in use for calculation of molecular electrostatic potential of proteins and parameterization of the electrostatic components of the force field parameters. Additionally I could dig up that there is some interest to electrostatic property calculations by density functional GGA methods employing Coulomb density fitting procedure, although it is not clear how important (or non important) are errors due to not use of the explicit Hartree-Fock exchange. Any comments a very welcome. With best regards, Victor. -- Victor Anisimov FQS Poland, Krakow ================================================ From: "Bosco" > Do you know the paper: M.D. beachy et al JACS, 119,5908-5920(1997). > There you may find on page 5917 arguments why one should use HF/6-31G* > charges on molecular parametrization process. From: "elewars" > I think it makes little difference whether you use HF/6-31G* or the faster > HF/3-21G for electrostatic properties. Compare some test jobs. Since you use > programs like Amber and Charmm, I believe you are doing single-point > calculations on geometries obtained by MM. From chemistry-request@server.ccl.net Fri Jul 12 10:01:38 2002 Received: from shardagate.mahindrabt.com ([206.102.1.162]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6CE1ac28703 for ; Fri, 12 Jul 2002 10:01:37 -0400 Received: from mahindrabt.com (mailscan.sharda.mahindrabt.com [10.5.0.97]) by shardagate.mahindrabt.com (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) with ESMTP id TAA18738 for ; Fri, 12 Jul 2002 19:31:32 +0530 X-SMTP-Sending-IP: 10.5.0.15 Received: from intranet.sharda.mahindrabt.com by mahindrabt.com ; 12 Jul 2002 19:25:46 +0530 Received: from mahindrabt.com ([10.5.2.39]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id TAA12299 for ; Fri, 12 Jul 2002 19:31:24 +0530 Message-ID: <3D2EE104.EA62E56F@mahindrabt.com> Date: Fri, 12 Jul 2002 19:30:36 +0530 From: "Dr. Sudhir A. Kulkarni" Organization: Mahindra British Telecom Limited X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: QSAR equation Content-Type: multipart/mixed; boundary="------------78071EB3820C817E79D86BEA" This is a multi-part message in MIME format. --------------78071EB3820C817E79D86BEA Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I was wondering about one thing which could be a simple query for many of you. What is the significance of cross correlation of independent terms in a QSAR equation generated using multiple regression? If I have a QSAR equation with high cross correlation of independent terms but the prediction of test compounds are good, should I consider this equation seriously? Any suggestion or literature reference on this would be highly appreciated. Thanks. Sudhir ********************************************************* Disclaimer This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and are hereby notified that any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited. ********************************************************* Visit us at http://www.mahindrabt.com --------------78071EB3820C817E79D86BEA Content-Type: text/x-vcard; charset=us-ascii; name="sudhirk.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Dr. Sudhir A. Kulkarni Content-Disposition: attachment; filename="sudhirk.vcf" begin:vcard n:Kulkarni;Dr. Sudhir A. tel;fax:+91-20-542-4466 tel;work:+91-20-401-8350 x-mozilla-html:FALSE url:www.mahindrabt.com org:Mahindra British Telecom Limited;Research and Development version:2.1 email;internet:sudhirk@MahindraBT.com title:Consultant adr;quoted-printable:;;Sharda Center, Off Karve Road=0D=0AErandwane;Pune;Maharashtra;411 004;India x-mozilla-cpt:;32608 fn:Dr. Sudhir A. Kulkarni end:vcard --------------78071EB3820C817E79D86BEA-- From chemistry-request@server.ccl.net Fri Jul 12 04:46:31 2002 Received: from ws05.pc.chemie.tu-darmstadt.de ([130.83.242.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6C8kUc22026 for ; Fri, 12 Jul 2002 04:46:30 -0400 Received: from pc.chemie.tu-darmstadt.de (pc2d.pc.chemie.tu-darmstadt.de [130.83.242.27]) by ws05.pc.chemie.tu-darmstadt.de (SGI-8.9.3/8.9.3) with ESMTP id KAA68902; Fri, 12 Jul 2002 10:46:27 +0200 (CDT) Message-ID: <3D2E9751.7206D980@pc.chemie.tu-darmstadt.de> Date: Fri, 12 Jul 2002 10:46:09 +0200 From: Bernd Schilling Reply-To: bernds@pc.chemie.tu-darmstadt.de Organization: Technische =?iso-8859-1?Q?Universit=E4t?= Darmstadt X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Tim =?iso-8859-1?Q?J=F6dicke?= , CCL Mailinglist Subject: Re: CCL:Molecular vs. Macroscopic Properties References: <3.0.1.32.20020710212807.006f1218@pop.uni-muenster.de> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Tim It is possible to correlate the sweetness of molecules with partial surface integrals of a surface related function which we call free energy surface density (FESD). Our method is in principle an extrapolation of the macroscopic free energy of binding or transfer to the solvent accessible surface of a molecule. You can find a discussion of the method and an application to sweetness recognition of some sucrose derivates in our paper: R. J鋑er, F. Schmidt, B. Schilling, J. Brickmann, Localization and quantification of hydrophobicity: The molecular free energy density (MolFESD) concept and its application to sweetness recognition, J. Comput.-Aided Mol. Design, 14 (2000) 631. I hope this will help you Bernd Tim J鰀icke wrote: > > Dear CCL's, > > i need some literature according the relationship of molecular vs. macroscopic > properties. E.g. the vdW-surface of a molecule and its sweetnes. > > Thanks in advance > > tim > > ******************************************************** > Tim J鰀icke > email: jodickt@uni-muenster.de > .... my brain hurts! Terry Gilliam > ******************************************************** > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Bernd Schilling Physical Chemistry I, Darmstadt University of Technology Petersenstr. 20, 64287 Darmstadt, Germany phone: <+int> 49 6151 163746, fax: <+int> 49 6151 164298 http://www.pc.chemie.tu-darmstadt.de/authors/bernds From chemistry-request@server.ccl.net Fri Jul 12 11:04:20 2002 Received: from sina.com ([202.108.35.251]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6CF4Jc29929 for ; Fri, 12 Jul 2002 11:04:20 -0400 Received: (qmail 604 invoked by uid 99); 12 Jul 2002 14:55:07 -0000 Message-ID: <20020712145507.603.qmail@sina.com> From: shengcq To: chemistry@ccl.net Subject: help MIME-Version: 1.0 Date: Fri, 12 Jul 2002 22:55:07 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Hello I have been studying the interaction between azole antifungals and P450 cytochrome lanosterol 14α-demethylase using InsightII/docking module.But the parameter of Fe is not available in CVFF forcefield and the coordination between inhibitor and Fe cannot be evaluated in Docking module.Could you give me some suggestion or give me the parameter of Fe in CVFF forcefild? Thank you! ______________________________________ =================================================================== 新浪免费电子邮箱 (http://mail.sina.com.cn) 新浪分类信息：二手市场走一走，该出手时就出手！ (http://classad.sina.com.cn/2shou/) From chemistry-request@server.ccl.net Fri Jul 12 14:15:47 2002 Received: (from root@localhost) by server.ccl.net (8.11.6/8.11.0) id g6CIFlr00776 for chemistry@ccl.net; Fri, 12 Jul 2002 14:15:47 -0400 Message-Id: <200207121815.g6CIFlr00776@server.ccl.net> Date: Fri, 12 Jul 2002 20:10:18 +0200 From: Bimo Ario Tejo To: chemistry@ccl.net Subject: CCL:different basis sets for Gaussian Hi CCLers, Is it any effect if I use different basis sets for optimisation and point calcu$ Regards, Bimo -- Get your free email from www.linuxmail.org Powered by Outblaze From chemistry-request@server.ccl.net Fri Jul 12 14:16:27 2002 Received: from ws4-4.us4.outblaze.com ([205.158.62.105]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6CIGRr00813 for ; Fri, 12 Jul 2002 14:16:27 -0400 Received: (qmail 16603 invoked by uid 1001); 12 Jul 2002 18:16:22 -0000 Message-ID: <20020712181622.16602.qmail@linuxmail.org> Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: MIME-tools 5.41 (Entity 5.404) Received: from [129.69.145.79] by ws4-4.us4.outblaze.com with http for bimo7@linuxmail.org; Fri, 12 Jul 2002 20:16:22 +0200 From: "Bimo Ario Tejo" To: chemistry@ccl.net Date: Fri, 12 Jul 2002 20:16:22 +0200 Subject: CCL:different basis sets for Gaussian X-Originating-Ip: 129.69.145.79 X-Originating-Server: ws4-4.us4.outblaze.com Hi CCLers, Is it any effect if I use different basis sets for optimisation and point calculation? I did hf/sto-3g optimisation and want to use hf/6-31g* basis set for pop=mk calculation (Gaussian 98) and use the result for RESP calculation (Amber). Is it tolerable to do that? Is it any significant differences if I use hf/6-31g* for optimisation? Regards, Bimo -- Get your free email from www.linuxmail.org Powered by Outblaze From chemistry-request@server.ccl.net Fri Jul 12 15:06:22 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6CJ6Mr01538 for ; Fri, 12 Jul 2002 15:06:22 -0400 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g6CJ6LqX009787 for ; Fri, 12 Jul 2002 16:06:21 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Fri Jul 12 16:01:31 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id QAA03117; Fri, 12 Jul 2002 16:06:21 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Fri, 12 Jul 2002 16:06:21 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: Number of Atom Types allowed by Autodock Message-ID: <3D2DB4B4@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Fellow CCLers, A question on Autodock and the number of atom types allowed in the ligand used for docking. My ligand contains Carbon, Aromatics, Nitrogen, Oxygen, Sulphur, Hydrogens, and Fluorine atoms. Apparently Autodock allows only 7 atom types. When I try to run the docking with this particular ligand, I get the following error message: autodock3: ERROR: ERROR: 7 atom types declared in "", S_line "CANOSHF"; maximum allowed is 6. Change "ATOM_MAPS" in "autocomm.h" autodock3: Aborting... autodock3: Unsuccessful Completion. I found two "autocomm.h" files, and also another called autocomm.h-extra-maps, however changing the contents of the autocomm.h files did not correct the problem. My questions are: 1- Can autodock support more than 6 different atom types per ligand 2- Am I going to have to recompile Autodock in order to be able to use ligands with more than 6 atom types. I will post the answers to the board. Thank you in advance. Robert ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ******************************** From chemistry-request@server.ccl.net Fri Jul 12 15:58:50 2002 Received: from mail.csusb.edu ([139.182.2.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6CJwor02798 for ; Fri, 12 Jul 2002 15:58:50 -0400 Received: from mail.csusb.edu (localhost [127.0.0.1]) by mail.csusb.edu (8.12.5/8.12.5) with ESMTP id g6CJvD5j015421; Fri, 12 Jul 2002 12:57:13 -0700 (PDT) Received: from localhost (kcousins@localhost) by mail.csusb.edu (8.12.5/8.12.5/Submit) with SMTP id g6CJvCgc015413; Fri, 12 Jul 2002 12:57:12 -0700 (PDT) Date: Fri, 12 Jul 2002 12:57:12 -0700 (PDT) From: Kimberley Cousins To: "Dr. Sudhir A. Kulkarni" cc: chemistry@ccl.net Subject: Re: CCL:QSAR equation In-Reply-To: <3D2EE104.EA62E56F@mahindrabt.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I was just reading a review that addresses this, in 'Reviews in Computational Chemistry" volume 11. See http://chem.iupui.edu/~boyd/rcc.html Kimberley Cousins Associate Professor of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@csusb.edu http://chem.csusb.edu/~kcousins On Fri, 12 Jul 2002, Dr. Sudhir A. Kulkarni wrote: > Hi, > I was wondering about one thing which could be a simple query for > many of you. > What is the significance of cross correlation of independent terms in a > QSAR equation generated using multiple regression? > If I have a QSAR equation with high cross correlation of independent > terms but the prediction of test compounds are good, should I consider > this equation seriously? > Any suggestion or literature reference on this would be highly > appreciated. > Thanks. > > Sudhir > > ********************************************************* > Disclaimer > > This message (including any attachments) contains > confidential information intended for a specific > individual and purpose, and is protected by law. > If you are not the intended recipient, you should > delete this message and are hereby notified that > any disclosure, copying, or distribution of this > message, or the taking of any action based on it, > is strictly prohibited. > > ********************************************************* > Visit us at http://www.mahindrabt.com From chemistry-request@server.ccl.net Fri Jul 12 16:32:51 2002 Received: (from root@localhost) by server.ccl.net (8.11.6/8.11.0) id g6CKWpQ03671; Fri, 12 Jul 2002 16:32:51 -0400 Received: from zeus.biomol.uci.edu (zeus.biomol.uci.edu [128.195.179.142]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g6CKFv116854 for ; Fri, 12 Jul 2002 16:15:57 -0400 (EDT) Received: from uci.edu (heffron@athena.biomol.uci.edu [128.195.179.141]) by zeus.biomol.uci.edu (8.9.3/) with ESMTP id UAA1695505 for ; Fri 12 Jul 2002 20:15:48 GMT Sender: heffron@uci.edu Message-ID: <3D2F38F3.D7A76908@uci.edu> Date: Fri, 12 Jul 2002 13:15:47 -0700 From: Susan Heffron Reply-To: sheffron@uci.edu Organization: UCI To: chemistry@ccl.net Subject: Errors when docking ligand References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Robert and CCL, > When I try to run the docking with this particular ligand, I get the following > error message: > > autodock3: ERROR: ERROR: 7 atom types declared in "", S_line "CANOSHF"; > maximum allowed is 6. > Change "ATOM_MAPS" in "autocomm.h" > autodock3: Aborting... I solved this problem by re-compiling autodock. The change required is in the file autocomm.h: change line: #define ATOM_MAPS 6 to be: #define ATOM_MAPS 8 (or however many you need) It sounds like you made this change to autocomm.h already. What is then required is to re-compile the program by typing the command "make". Susan Heffron P.S. In my particular case, on an SGI, I had to make the following changes to the Makefile to get it to run without error messages: old line: OLIMIT = $(CSTD) $(OPT) # SGI, Sun, HP, Convex, ... new line: OLIMIT = $(CSTD) $(OPT) -OPT:Olimit=2442 # Some SGIs. old line: DBUG = -DNDEBUG # No debugging and no assert code. new line: DBUG = # Use assert code. ========================================================================== Thanks, Susan Heffron