From chemistry-request@server.ccl.net Tue Nov 2 11:17:29 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 LAA01320 for ; Tue, 2 Nov 1999 11:17:29 -0500 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 VAA14819 for ; Mon, 28 Jun 1999 21:47:25 -0700 Sender: anil@ozone.umsl.edu Message-ID: <381F29B9.B4F30B51@ozone.umsl.edu> Date: Tue, 02 Nov 1999 10:13:13 -0800 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: Re: CCL:receptor flexibility in CADD References: <381EBB43.339DEC20@chemcca10.ucsd.edu> Content-Type: text/plain; charset=x-UNICODE-2-0-UTF-7 Content-Transfer-Encoding: 7bit Please check this website for a study related to : http://www.hughesinstitute.org/pages/hiv_inhibitors.html Thanks, Anil. Heather A. Carlson wrote: > Hello All, > > We all know that it is a limitation to use a single protein structure > to represent a target site on a protein. However, many of us still use > that approach as there is no accepted way of accommodating the inherent > flexibility of an active site in computer aided drug design. There are > many means of accommodating ligand flexibility... I am interested in > receptor flexibility. > > I've recently developed a method for superimposing multiple protein > conformations to represent the inherent flexibility of a receptor when > developing a complementary pharmacophore model (an ASAP article is > available through J Phys Chem A: Carlson, Masukawa, McCammon). The > only other work I have found that is at all similar is a ligand docking > study by Knegtel, Kuntz, and Oshiro (J Mol Biol 1997, 266, 424-440) > which introduces weighting methods either for the interaction energy > between a ligand and the receptor or in the description the geometry of > the site. > > Does anyone know of methods for accommodating an ensemble of protein > conformations? Has anyone tried a similar idea without success or know > of particularly interesting cases where the lack of protein flexibility > leads to incorrect predictions? > > Thank you, > Heather > ___________________________________________________________________ > Dr. Heather A. Carlson, Ph.D. > American Cancer Society Postdoctoral Fellow > La Jolla Interfaces in Science - BWF Postdoctoral Fellow > > UCSD, Dept. of Chemistry and Biochemistry Phone: (858) 822-1469 > 9500 Gilman Drive, 4202 Urey Hall Fax: (858) 534-7042 > La Jolla, CA 92093-0365 E-mail: hcarlson@chemcca10.ucsd.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 -- -------------------------------------------------------------- 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 Tue Nov 2 18:23:53 1999 Received: from eagle.prod.itd.earthlink.net (eagle.prod.itd.earthlink.net [207.217.120.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA02837 for ; Tue, 2 Nov 1999 18:23:52 -0500 Received: from lrz.uni-muenchen.de (1Cust34.tnt1.rancho-cucamonga.ca.da.uu.net [63.24.225.34]) by eagle.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id PAA08343 for ; Tue, 2 Nov 1999 15:18:38 -0800 (PST) Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id QAA08931 for ; Tue, 2 Nov 1999 16:16:07 -0800 Resent-From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Resent-Message-ID: <14367.32455.795254.481916@lrz.uni-muenchen.de> Resent-Date: Tue, 2 Nov 1999 16:16:07 -0800 (PST) Resent-To: Message-Id: <19991021xxx1342.JAA18742@tick.physics.ncsu.edu> Precedence: bulk From: To: beowulf@beowulf.gsfc.nasa.gov Subject: Athlon optimized BLAS routines Date: Thu, 21 Oct 1999 09:42:39 -0400 (EDT) From: Emil Briggs I've written a set of Athlon optimized double precision BLAS1 routines in assembly. The source can be found at http://nemo.physics.ncsu.edu/~briggs/blas_src_v0.11_tar.gz The routines are in an early stage of development but they do pass the Level 1 Blas testing routines from netlib and they work correctly in the applications I've tested. Thats not a guarantee that they are correct in all cases however so use with caution. The routines use the Athlon memory prefetch instructions which really boost performance for large data sets. (You'll get an illegal instruction exception on PentiumIII systems). I'm still tuning, optimizing and debugging but these are already much faster on an Athlon than any other set of BLAS1 libs that I know of available for Linux. Regards Emil ------------------------------------------------------------------ Benchmark results on a 500Mhz Athlon system. Best time of 20 iterations. Intel optimized libraries are version lsblasppro1.1o_08.99.a courtesy of Greg Henry. DAXPY ********************************************************** N Athlon libs Intel optimized 4096 411.49 373.48 16384 109.60 82.35 65536 57.49 49.29 262144 52.66 43.67 1048576 51.31 43.66 DDOT ********************************************************** N Athlon libs Intel optimized 4096 587.35 164.40 16384 155.30 72.18 65536 80.81 42.39 262144 75.72 28.76 1048576 74.79 26.16 DSCAL ********************************************************** N Athlon libs Intel optimized 4096 293.67 164.40 16384 91.50 72.18 65536 58.36 42.39 262144 44.73 28.76 1048576 42.25 26.16 DNRM2 ********************************************************** N Athlon libs Intel optimized 4096 630.45 545.39 16384 394.94 338.10 65536 182.55 116.71 262144 156.92 72.56 1048576 153.80 65.74 DCOPY ********************************************************** N Athlon libs Intel optimized 4096 4398.05 2421.83 16384 888.85 515.11 65536 539.97 324.83 262144 449.60 308.21 1048576 445.05 298.25 ------------------------------------------------------------------- To unsubscribe send a message body containing "unsubscribe" to beowulf-request@beowulf.org From chemistry-request@server.ccl.net Wed Nov 3 04:07:52 1999 Received: from linux2.ipc.pku.edu.cn (taop@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA05115 for ; Wed, 3 Nov 1999 04:07:49 -0500 Received: from localhost (taop@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id RAA18907 for ; Wed, 3 Nov 1999 17:07:01 +0800 Date: Wed, 3 Nov 1999 17:07:01 +0800 (CST) From: Tao Peng To: ccl Subject: CCL:Free CADD software release: PLOGP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, May I draw your attention now? We announce here that the program package PLOGP is now available. You can download it free via anonymous FTP to ftp2.ipc.pku.edu.cn/pub/software/plogp/. PLOGP is an residue-additive method for calculating the octanol/water partition coefficient(logP) of peptide less than hexapeptide. It gives the logP and logD value for a give peptide by summing the contributions from residues and correction factors. Our work of PLOGP has been published: Calculating Partition Coefficients of Peptides by the Addition Method Peng Tao, Renxiao Wang, and Luhua Lai J. Mol. Model. 1999, 5, 189-195. To know more about the program package PLOGP, please visit the site: http://mdl.ipc.pku.edu.cn/~taop/achievement/plogp/PLOGP_MANUAL.html PLOGP is written in C and has been tested on UNIX, and LINUX platforms. If you encounter any problem while downloading the program, please contact Mr. Peng Tao at . Please forward this mail to anyone who may concern. With best wishes, Molecular Design Laboratory, Institute of Physical Chemistry Peking University, Beijing, China Yours Sincerely Tao Peng \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* \* Tao Peng \ \* \* Molecular Design Laboratory \ E-mail:taop@mdl.ipc.pku.edu.cn \* \* Institute of Physical Chemistry \ Lab Phone: 86-10-62756833 \* \* Peking University \ Fax Number:86-10-62751725 \* \* Beijing, 100871 \ http://mdl.ipc.pku.edu.cn/~taop \* \* P.R.China \ Dormitory Phone: 86-10-62761206 \* \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* From chemistry-request@server.ccl.net Wed Nov 3 07:16:35 1999 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06752 for ; Wed, 3 Nov 1999 07:16:35 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id MAA20712 for ; Wed, 3 Nov 1999 12:11:24 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Wed, 3 Nov 1999 12:11:24 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: MP2 in solids Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have come across a problem in which it would be useful to perform a correlated calculation on a solid since the errors in LDA are too large. I have not seen any codes which carry out MP2 in a solid. Is there some fundamental numerical or theoretical reason for this? Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Wed Nov 3 09:42:02 1999 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07584 for ; Wed, 3 Nov 1999 09:42:01 -0500 Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with SMTP id PAA22817 for ; Wed, 3 Nov 1999 15:36:40 +0100 (MET) Received: from pc03.chemie.uni-jena.de by pc04.chemie.uni-jena.de (5.65v3.2/1.1.10.5/28Jan98-0152PM) id AA08933; Wed, 3 Nov 1999 15:36:39 +0100 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <3820487A.63DE@pc04.chemie.uni-jena.de> Date: Wed, 03 Nov 1999 15:36:42 +0100 From: Andreas Goeller X-Mailer: Mozilla 3.04Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: CHEMISTRY@ccl.net Subject: energy decomposition Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I'm looking for a method for intramolecular energy decomposition, which is able to give the various contributions to the total energy of rotational barriers like e.g. the ones in ethane, ethene ... The decomposition schemes of Morokuma and also of Ziegler seem to be applicable only for intermolecular interactions, as is the version available in Gamess. With NBO analysis I get Fock matrix energy terms for various bond bond interactions, but here it seems that I am restricted to one localized mesomeric structure. I would like to have a consistent measure of steric, bonding and antibonding, mesomeric contributions to total energy. Is there any program available that can do this? -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Nov 3 11:28:13 1999 Received: from nano.chem.nwu.edu (nano.chem.nwu.edu [129.105.14.190]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA08191 for ; Wed, 3 Nov 1999 11:28:13 -0500 Received: from nano.chem.nwu.edu ([129.105.14.190]) by nano.chem.nwu.edu (WESMTP 2.1 [Sep 22 1998]) with SMTP id 226029656; Wed, 03 Nov 1999 16:30:07 GMT Date: Wed, 03 Nov 1999 10:30:04 -0600 From: "G. Rechtsteiner" Subject: ZINDO Parameters To: CHEMISTRY@ccl.net Message-Id: <4.2.0.58.19991103102859.00a31100@nano.chem.nwu.edu> X-Sender: greg@nano.chem.nwu.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello: I have a colleague looking for the following: >What I need are the ZINDO/S parameters for chlorine. The >values for the two-electron, one-center Coulomb integrals would be most >handy, as it seems that those are the ones that Hyperchem 5 is lacking. > >I'm running these calculations on a mixed valence compound in an organic >cyclic framework. It has a total of 70 atoms. The molecule has two >ruthenium ions in it, each to which two chlorides are ligated. At the >moment, I'm using fluorides instead. Thank you, Greg Rechtsteiner From chemistry-request@server.ccl.net Wed Nov 3 11:13:24 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA08117 for ; Wed, 3 Nov 1999 11:13:23 -0500 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id RAA23739; Wed, 3 Nov 1999 17:07:54 +0100 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: "eugene.leitl" , beowulf@beowulf.gsfc.nasa.gov, CCL Subject: Re: CCL:Athlon optimized BLAS routines Date: Wed, 3 Nov 1999 17:04:34 +0100 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <19991021xxx1342.JAA18742@tick.physics.ncsu.edu> In-Reply-To: <19991021xxx1342.JAA18742@tick.physics.ncsu.edu> MIME-Version: 1.0 Message-Id: <99110317075304.08167@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA08118 On Don, 21 Okt 1999 eugene.leitl wrote: >From: Emil Briggs > >I've written a set of Athlon optimized double precision >BLAS1 routines in assembly. The source can be found at > >http://nemo.physics.ncsu.edu/~briggs/blas_src_v0.11_tar.gz [snip] >I'm still tuning, optimizing and debugging but these are already >much faster on an Athlon than any other set of BLAS1 libs that >I know of available for Linux. Faster than Compaq's cxml stuff on a 264 machine ? Sorry, I do not have the numbers, since I only have a 164 machine. Just beeing curious :-) -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Wed Nov 3 11:40:13 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA08340 for ; Wed, 3 Nov 1999 11:40:13 -0500 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id IAA24697 for ; Wed, 3 Nov 1999 08:32:44 -0800 (PST) Received: from localhost (yadavm@localhost) by elvis.scripps.edu (8.9.2/TSRI-3.0) with SMTP id IAA186152 for ; Wed, 3 Nov 1999 08:32:44 -0800 (PST) Date: Wed, 3 Nov 1999 08:32:44 -0800 (PST) From: Maneesh Yadav To: chemistry@ccl.net Subject: Mismatched base pair conformation? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, We are trying to get a decent picture of the conformation of a duplex DNA string with a small internal reigon of mismatched base pairs, can anyone comment on some good tools/ways to do this? I can run minimzations through insightII, but I don't think I can do a decent job with the forcefields that you can run minimizations with (if anyone would like to tell me other wise, please do). -Many Thanks, Maneesh Yadav From chemistry-request@server.ccl.net Wed Nov 3 15:24:00 1999 Received: from castor.rice.edu (castor.rice.edu [128.42.81.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA09408 for ; Wed, 3 Nov 1999 15:24:00 -0500 Received: from localhost (knk@localhost) by castor.rice.edu (AIX4.3/8.9.3/8.9.3) with ESMTP id OAA11900; Wed, 3 Nov 1999 14:18:50 -0600 Date: Wed, 3 Nov 1999 14:18:50 -0600 (CST) From: "Konstantin N. Kudin" To: Andrew Horsfield cc: Computational Chemistry List Subject: Re: CCL:MP2 in solids In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 3 Nov 1999, Andrew Horsfield wrote: > Hi, > > I have come across a problem in which it would be useful to perform a > correlated calculation on a solid since the errors in LDA are too large. I > have not seen any codes which carry out MP2 in a solid. Is there some > fundamental numerical or theoretical reason for this? > > Cheers, > > Andrew > It seems that so far MP2 method has been implemented for polymers only. Check the following paper: "Analytical energy gradients in second-order Moller-Plesset perturbation theory for extended systems" S. Hirata and S. Iwata, J. Chem. Phys. 109, 4147 (1998). The paper references most of the people working in this area. Specifically, these are S. Suhai J. Q. Sun and R. J. Bartlett S. Hirata and S. Iwata Sun and Bartlett did some studies about convergence of the required MO integrals: Second-order many-body perturbation-theory calculations in extended systems. Author: Sun, Jun-Qiang; Bartlett, Rodney J. Source: J. Chem. Phys. Year:1996 Convergence of many-body perturbation methods with lattice summations in extended systems. Author: Sun, Jun-Qiang; Bartlett, Rodney J. Source: J. Chem. Phys. Year:1997 Convergence Behavior of Many-Body Perturbation Theory with Lattice Summations in Polymers. Author: Sun, Jun-Qiang; Bartlett, Rodney J. Source: Phys. Rev. Lett. Year:1998 Regards, Konstantin Kudin From chemistry-request@server.ccl.net Wed Nov 3 15:59:46 1999 Received: from mercury.chem.nwu.edu (rassolov@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA09585 for ; Wed, 3 Nov 1999 15:59:46 -0500 Received: from localhost by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id OAA04843 for ; Wed, 3 Nov 1999 14:57:41 -0600 (CST) Date: Wed, 3 Nov 1999 14:57:41 -0600 (CST) From: Vitaly Rassolov To: Computational Chemistry List Subject: RE: MP2 in solids Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It was well known (but mostly forgotten by many) that MP2 energy diverges for the electron gas. The same is probably true for the solids with small HOMO-LUMO gap. Even the presence of very diffuse orbitals in molecules often deteriorates MP2 energy. That is probably the reason of lack of MP2 calculations in solids. _______ Vitaly Rassolov rassolov@chem.nwu.edu Chemistry Department tel. (847) 491-3423 Northwestern University fax (847) 491-7713 From chemistry-request@server.ccl.net Wed Nov 3 17:42:53 1999 Received: from sumter.awod.com (sumter.awod.com [198.81.225.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA10204 for ; Wed, 3 Nov 1999 17:42:52 -0500 Received: from [208.140.98.72] (wa0072.tnt1.awod.com [208.140.98.72]) by sumter.awod.com (8.8.7/8.8.8) with SMTP id RAA22844; Wed, 3 Nov 1999 17:37:23 -0500 (EST) (envelope-from netsci@awod.com) Date: Wed, 3 Nov 1999 17:37:23 -0500 (EST) X-Sender: arichon@awod.com (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: netsci@awod.com (Network Science) Subject: Final Programs-2000 Charleston Conferences Network Science Corporation announces the final programs for The 2000 Charleston Conferences: February 28-March 1 Innovative Techniques in New Lead Discovery and Development March 1-3 Research Perspectives in Computational and Structural Chemistry The complete program for each meeting with on-line registration forms is available at http://www.netsci.org, or send e-mail to editors@netsci.org for details. The deadline for Student Stipend Award entries is November 30, 1999.