From bioinfo.ernet.in!sangeeta@bioinfo.ernet.in Mon Jul 6 03:44:44 1998 Received: from naveen.ncst.ernet.in (naveen.ncst.ernet.in [202.41.110.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA04078 Mon, 6 Jul 1998 03:44:28 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id NAA17483 for ; Mon, 6 Jul 1998 13:16:44 +0530 Received: by iucaa (5.65v3.2/SMI-4.1) id AA26076; Mon, 6 Jul 1998 13:11:17 +0500 Received: by (5.x/SMI-SVR4) id AA01165; Mon, 6 Jul 1998 13:03:02 -0500 Date: Mon, 6 Jul 1998 23:03:00 +0500 (GMT-5) From: Sangeeta Sawant To: CHEMISTRY@www.ccl.net Subject: Wanted program for superimposing peptides/proteins Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! I would like to know if there is any software/program (preferably shareware/public-domain) which allows to superimpose several protein/peptide conformations onto one (say, template confo.) in a "batch mode". The program may be for either IRIX or OS2 (DEC-ALPHA) or SOLARIS or LINUX or DOS (No Mac-OS please). Any help will be appreciated. Thanks in advance. Sangeeta +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Mrs. Sangeeta Sawant + + Research Fellow email : sangeeta@bioinfo.ernet.in + + Bioinformatics Centre phone : +91-212-355039 + + University of Pune fax : +91-212-350087 + + Ganeshkhind + + Pune - 411007 + + India. + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From d.pender@surrey.ac.uk Mon Jul 6 07:29:56 1998 Received: from mailc.surrey.ac.uk (mailc.surrey.ac.uk [131.227.100.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA05488 Mon, 6 Jul 1998 07:29:53 -0400 (EDT) Received: from surrey.ac.uk (actually host pc096.chem.surrey.ac.uk) by mailc.surrey.ac.uk with SMTP-external (PP) with ESMTP; Mon, 6 Jul 1998 12:29:41 +0100 Message-ID: <35A0B636.303E6EB8@surrey.ac.uk> Date: Mon, 06 Jul 1998 12:34:14 +0100 From: Dave Organization: University of Surrey X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Negative eigenvalues in an IRC Calcn! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings, This is my debut on CCL so please excuse my nerves! I have been doing some ab initio calculations recently on the ring opening of cyclobutene using GAUSSIAN94. I have completed an optimisation of the transition state corresponding to the ring opening and formation of the TRANS product (trans-butadiene). To check that the transition state corresponds to the trans conformation an IRC calculation was performed to follow the path in the direction TOWARDS (reverse direction) the trans product. The command line was: >> # RHF/6-31G(d) IRC(CalcFC,Reverse,Stepsize=40,maxpoints=24) The calculation stopped on the 12th point along the path after 5 optimisation steps having failed to converge with this unusual message: >> Optimization stopped. >> -- Wrong number of negative eigenvalues: Desired= 0 Actual=*** This is very peculiar - I have never seen this before. It is highly unlikely that the calculation has 'stumbled upon' another saddle point. Has anyone come across this before? Any reasons/suggestions/ideas would be welcomed. Thank you for your time, Dave P. __________________________________________________________ Dave Pender Tel. 01483 259591 Department of Chemistry Pager. 0336 785185 University of Surrey Guildford Surrey, UK GU2 5XH. ** "The World is a Stage, but the Play is Badly Cast" -- Oscar Wilde ** From lin@chu1.chem.nthu.edu.tw Mon Jul 6 08:22:20 1998 Received: from chu1.chem.nthu.edu.tw (Chu1.Chem.nthu.edu.tw [140.114.45.236]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA05908 Mon, 6 Jul 1998 08:22:09 -0400 (EDT) Received: by chu1.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA19385; Mon, 6 Jul 1998 20:15:02 +0800 From: lin@chu1.chem.nthu.edu.tw (Chiu-Ling Lin) Message-Id: <9807061215.AA19385@chu1.chem.nthu.edu.tw> Subject: NBO in G94? To: CHEMISTRY@www.ccl.net Date: Mon, 6 Jul 98 20:15:02 TAIST X-Mailer: ELM [version 2.4dev PL17] I had typed the keyword "NBORead" in my input(I had finished the frequency calculation) to calculate the Wiberg and atom-atom overlap-weighted NAO bond order, but the output didn't give what I want. The input was written as following, ************************************ $rungaussian %chk=h2 #n b3lyp/6-31g** scf=direct pop=nboread scfcyc=100 guess=read geom=check -------h2co-h2-ts------------- 0 1 ************************************* Is anything wrong in the input? And how can I get the "bond indexs"? Thanks to all who responded. =============================================== Chiu-Ling Lin Department of Chemistry, Nthu, Hsinchu, Taiwan lin@chu.chem.nthu.edu.tw lin@chu1.chem.nthu.edu.tw =============================================== From gostowskir@apsu01.apsu.edu Mon Jul 6 09:51:31 1998 Received: from apsu02.apsu.edu (apsu02.apsu.edu [198.146.56.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA06878 Mon, 6 Jul 1998 09:51:31 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IZ2OUH7THS003BIJ@APSU02.APSU.EDU> for chemistry@www.ccl.net; Mon, 6 Jul 1998 08:49:21 CST Date: Mon, 06 Jul 1998 08:53:45 -0500 From: Rudy Gostowski Subject: determination of geometry when a low barrier to rotation is present To: CCL LIST Message-id: <01IZ2OUH8GSY003BIJ@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal We are using GAMESS to determine the geometry of 9-aryl substituted fluorenyl radicals. When the aryl group is phenyl the barrier to rotation appears to be small and the structure is uncertain. Please suggest the best way to find the true minimum for this molecule (unpaired electron on carbon in parenthesis): ::C: C C : :: C C ::C: : ::C : : (C) : : C:: C C C C : :: :: : C C : C C ::C : : C:: This needs to be accomplished at an ab intio level rather than semi-empirical (MOPAC). Your help with this is appreciated. Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 931-648-7624 FAX 931-648-5996 gostowskir@apsu01.apsu.edu From goeller@pc04.chemie.uni-jena.de Mon Jul 6 10:39:39 1998 Received: from cnve.rz.uni-jena.de (root@cnve.rz.uni-jena.de [141.35.1.32]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA07685 Mon, 6 Jul 1998 10:39:33 -0400 (EDT) Received: from fsuj03.rz.uni-jena.de (root@fsuj03.rz.uni-jena.de [141.35.2.32]) by cnve.rz.uni-jena.de (8.8.7/8.8.7) with ESMTP id QAA25497 for ; Mon, 6 Jul 1998 16:39:13 +0200 (MESZ) Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj03.rz.uni-jena.de (8.7.1/8.6.10) with SMTP id QAA07466 for ; Mon, 6 Jul 1998 16:39:10 +0200 (MESZ) Received: from localhost by pc04.chemie.uni-jena.de (5.65v3.2/1.1.10.5/28Jan98-0152PM) id AA27532; Mon, 6 Jul 1998 16:39:29 +0200 Sender: goeller@pc04.chemie.uni-jena.de Message-Id: <35A0E1A0.41C6@pc04.chemie.uni-jena.de> Date: Mon, 06 Jul 1998 16:39:29 +0200 From: Andreas Goeller X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: C70 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, could anyone please send me the input for C70 in xyz or as Mopac- z-matrix? Thanks in advance -- 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 schrecke@t12.lanl.gov Wed Jul 1 14:26:52 1998 Received: from mailhost.lanl.gov (mailhost.lanl.gov [128.165.3.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA22564 Wed, 1 Jul 1998 14:26:51 -0400 (EDT) Received: from [128.165.22.209] (machgs.lanl.gov [128.165.22.209]) by mailhost.lanl.gov (8.8.8/(cic-5, 10/28/97)) with SMTP id MAA06598 for ; Wed, 1 Jul 1998 12:26:49 -0600 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 1 Jul 1998 12:28:01 -0600 To: CHEMISTRY@www.ccl.net (CCL) From: schrecke@t12.lanl.gov (Georg Schreckenbach) Subject: Summary: two-el. integrals from G94 Hi CCL readers, here is my summary for a recent CCL query, as requested by a number of people. I got two answers (many thanx to Doug Fox and Mike Frisch!) but I would also like to draw your attention to the related summery by Iraj Daizadeh, posted on the CCL just after my question (on June 15 -- well, at least that's the date when it reached me). I have copied it below. Best regards, Georg =========================================== Original question: is there a (hopefully easy) way to print out from GAUSSIAN a few two-electron integrals of the sort (ab|ij) or (ai|bj) where a and b are selected virtual MOs, and i and j are some occupied MOs? -- I use the usual definition for the integrals, namely: (pq|rs) = integral [psi_p(r1) * psi_q(r1)*(1/r12)*psi_r(r2)*psi_s(r2)*dr1*dr2 =========================================== Answers: From: gaussian.com!fox@lorentzian.com (Doug Fox) Date: Tue, 16 Jun 1998 12:53:33 -0400 (EDT) Georg, There is no option for selectively printing a few integrals. You can use %kjob l314 # ... SCF=Conventional ExtraLink=l316 NoRaff IOp(3/33=6) to get the integrals printed into the log file and then select out the ones you want. =========================================== From: frisch@lorentzian.com (Mike Frisch) Date: Tue, 16 Jun 1998 14:06:16 -0400 (EDT) There's no way to get selected MO integrals. If you run an MP2 calculation and turn up the print, these integrals will be printed out: mp2=semidirect iop33(9=4) force should do the trick. This will get you matrices of things like (ip|qr) for each i and p and all qr together. Alternatively, do a regular transformation, save the read-write file, and use the rwfdump utility to dump the appropriate parts of the file: %rwf=some-name mp2 use=l804 tran=iabc then rwfdump some-name.rwf - 2r will get you file 2, which has (ia|jb) in the order i (slowest running) jab (fastest running) similarly rwfdump some-name.rwf - 7r will get you file 7, which has (ij|ab) in the order i.le.j a.le.b (i.e., i=1 j=1 a=1 b=1, then i=1, j=1, a=1, b=2 ... 111V, where V is the number of virtuals, then 1122...1112V, and on up to 11VV, then 1211, etc up to OOVV, where O is the number of occupieds. Mike Frisch =========================================== And finally an excerpt from the mentioned other summary (see the CCL archives for the full posting): Resent-From: "Iraj Daizadeh" Resent-Date: Mon, 15 Jun 1998 15:46:52 -0700 Resent-To: schrecke@t12.LANL.GOV X-Authentication-Warning: www.ccl.net: mail set sender to chemistry-request@www.ccl.net using -f From: "Iraj Daizadeh" Date: Thu, 5 Mar 1998 09:34:01 -0800 To: CHEMISTRY@www.ccl.net Subject: CCL:G:Summary:G94 -> and Sender: Computational Chemistry List Hello. Here is a summary of those that replied to my query (see below) concerning the printing of two electron integrals from a conventional scf calculation. In general, to print out two electron integrals into a standard G94 output file is to insert the following keywords into the input deck: extralink=l316 NORAFF (for pure integrals - optional) and make sure that the SCF keyword is set to conventional. To simply save the binary file, see the last comment below. Thank you very much. Iraj. [rest of posting deleted. G.S.] -- ============================================================== Dr. Georg Schreckenbach Tel: (USA)-505-667 7605 Theoretical Chemistry T-12 FAX: (USA)-505-665 3909 M.S. B268, Los Alamos National E-mail: schrecke@t12.lanl.gov Laboratory, Los Alamos, New Mexico, 87545, USA Internet: http://www.t12.lanl.gov/~schrecke/ ============================================================== From correarj@hotmail.com Thu Jul 2 08:58:01 1998 Received: from hotmail.com (f85.hotmail.com [207.82.250.191]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA00525 Thu, 2 Jul 1998 08:58:01 -0400 (EDT) Received: (qmail 12769 invoked by uid 0); 2 Jul 1998 12:57:31 -0000 Message-ID: <19980702125731.12768.qmail@hotmail.com> Received: from 146.164.6.67 by www.hotmail.com with HTTP; Thu, 02 Jul 1998 05:57:31 PDT X-Originating-IP: [146.164.6.67] From: "Rodrigo Sal" To: chemistry@www.ccl.net Subject: Gamess problems! Content-Type: text/plain Date: Thu, 02 Jul 1998 05:57:31 PDT Hi CCL users ! Im using Gamess for the fist time and as it was expected, I have a lot of problems. But the most important is: How can I fix dihedrals in this software ??? Let me show what I've been doing. 1-In z-matrix the 4 dihedrals I want to fix are the in degrees, instead of variables. x y 1r1 z 2r2 1a1 w 3r3 2a2 1 180.00 (I want all of them with 180 degrees) And this same way for the others. 2- I created a comand line STATPT FREEZE(3)= 3,4,3,2,1 Here, I suppose FREEZE (3-> I dont know what it means).=3, means Im fixing dihedrals and the four following numbers are the atoms I suppose to be fixing. But after the calculation is done, the dihedrals are 1,1,2 and 5 degrees different from what I set. IS Gamess unable to fix some geometries or am I doing somethig wrong ? When I submit this job without these changes the dihedrals are completly different from each other and 180. Thanks your attention. Rodrigo Correa ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From tvd@msi.com Thu Jul 2 10:37:05 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA01387 Thu, 2 Jul 1998 10:37:04 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA00887; Thu, 2 Jul 98 07:36:31 -0700 Received: from unknown(146.202.0.104) by bioc1.msi.com via smap (V2.0) id xma000885; Thu, 2 Jul 98 07:36:24 -0700 Message-Id: <3.0.32.19980702073824.00a39d28@146.202.0.225> X-Sender: tvd@146.202.0.225 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 02 Jul 1998 07:38:26 -0700 To: CHEMISTRY@www.ccl.net From: Ton van Daelen Subject: Re: Data visualization software for MD sims Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Patrick - MSI's Cerius2 SDK allows you to visualize output from all sorts of modeling applications. It also provides tools for putting together a graphical UI to a stand alone application. Look at http://www.msi.com/support/sdk/ for more details. There is an examples section that contains a template for an interface to an MD program. Regards - Ton Patrick Brian Kohl wrote: > > My group is running a few molecular dynamics sims involving a few hundred > molecules each, and we need to invest in some data visualization software > to allow us to display images and animations of our sims. Something that > would accept as input the coordinates of the atoms involved would be > preferable, as would be a program that is easily modified. Has anyone had > any good/bad experiences with situations like this? Is there any notable > software that people have found especially useful for data viz? Thanks. Ton van Daelen, Ph.D. Product Manager Software Developer's Kit __o E: tvd@msi.com _`\<,_ Molecular Simulations, Inc P: -1-619-799-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com - Check out What's New in SDK on the SDK web pages at http://www.msi.com/support/sdk/ - A free Cerius2 interface to the program GRID is now available. Download it from the SDK website From yliu@mail.wesleyan.edu Thu Jul 2 10:49:08 1998 Received: from mail.wesleyan.edu (dns.wesleyan.edu [129.133.12.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA01566 Thu, 2 Jul 1998 10:49:07 -0400 (EDT) Received: from dkombo.wesleyan.edu (jellyfish.chem.wesleyan.edu [129.133.20.75]) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id KAA29531 for ; Thu, 2 Jul 1998 10:49:08 -0400 (EDT) Date: Thu, 2 Jul 1998 10:49:08 -0400 (EDT) Message-Id: <199807021449.KAA29531@mail.wesleyan.edu> X-Sender: yliu@wesleyan.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" To: chemistry@www.ccl.net From: Yongxing Liu Subject: Summary, Torsional MD Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id KAA01566 Dear Friends, Thanks a lot for answering my question. Here is the summary of the answers. Thanks again! ////////////////////////////////////////////////////////////////////////////// // The Question ///////////////////////////////////////////////////////////////////////////// I want to know if there exists one program that can perform Molecular Dynamics Simulation only in torsional space. I also want to know related algorithms and the degree of difficulty to implement such a program compared with normal Cartesian MD programs. I know some programs can do this by restrain bond length and bond angles, but this will have extra cost. Please correct me if I am wrong. /////////////////////////////////////////////ò//////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// I think Harold Scheraga's group published such an algorithm at least 6 or 8 years ago. (sorry I don't have the ref anymore). I recall the theory reminded me of automatic Talyor series expansion methods (Y.F. Chang, early 80's). Richard Cornell Theory Center /////////////////////////////////////////////ò//////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// > I think Harold Scheraga's group published such an algorithm > at least 6 or 8 years ago. (sorry I don't have the ref anymore). > I recall the theory reminded me of automatic Talyor series expansion methods > (Y.F. Chang, early 80's). The program is available from QCPE (qcp664). Be careful though, we never got it to compile because it requires some libraries we didn't have (and they cost $$). Cheers Michael /////////////////////////////////////////////ò//////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// Dear Yongxing, As you probably know, most computation chemistry program uses Cartesian coordinates (XYZ) for modelling of molecule instead of internal coordinates (bond length, bond angles and torsion angles). As I know, there are not program that operates internal coordinates. But using cartesian coordinates for torsional space development is hard because program have to recalculate ALL coordinates for changing only ONE torsion angle. On my opinion, for this principial reason calculating of torsional space in cartesian coordinates should have unsatisfactory accuracy. Now we are attempting to write program that uses internal coordinates, but even alpha version is not ready today. Vladimir. "Tikhonenko Vladimir" ////////////////////////////////////////////////////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// Hi, Just a quick note... try looking at a package called ICM. A wb search should pull it up. Cheers Ashley From: Ashley George ////////////////////////////////////////////////////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// check out Axel Bruenger's X-plor, they recently implemented torsion angle dynamics for protein structure refinement: Proteins 1994 Aug;19(4):277-290 Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Rice LM, Brunger AT Cheers, Ronald ------------------------------------------------------------------------------- Dr. Ronald M. A. Knegtel Research Scientist Dept. of Molecular Design and Informatics Phone : +31-412-661469 N.V. Organon, RK2340 Fax : +31-412-662539 P.O. Box 20 5340 BH Oss http://www.organon.nl/ The Netherlands E-Mail : r.knegtel@organon.oss.akzonobel.nl ------------------------------------------------------------------------------- ////////////////////////////////////////////////////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// the program XPLOR can perform torsion angle dynamics. Find info re XPLOR at http://www.NMR.EMBL-Heidelberg.DE/xplor/htmlman/ or at http://xplor.csb.yale.edu/xplor-info/xploronline.html The torsion dynamics part is described in a draft manuscript which seems not to have made it into the main docs so far. You might be interested in the references mentioned therein: 1) Bac, D.-S. and Haug, E.J. (1987) Mech. Struct. Mach. 15:359-382 2) Bac and Haug (1987), Mech. Struct. Mach. 15:481-506 3) Rice, L.M. and Bruenger, A.T. (1994) Proteins 19:277-290 The last reference is probably the most interesting for you. Regards, Lutz Ehrlich ______________________________________________________________________ Lutz Ehrlich email: lutz.ehrlich@embl-heidelberg.de EMBL web : http://www.embl-heidelberg.de/~ehrlich Meyerhofstr. 1 D-69012 Heidelberg phone: +49-6221-387-140 Germany fax : +49-6221-387-517 ////////////////////////////////////////////////////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// You might be interested in these two papers: G.R. Kneller, K. Hinsen Generalized Euler equations for linked rigid bodies Phys. Rev. E 50, 1559 (1994) K. Hinsen, G.R. Kneller Influence of constraints on the dynamics of polypeptide chains Phys. Rev. E 52, 6868 (1995) The first paper derives the equations of motions for a system with arbitrary distance constraints using generalized coordinates (torsion angle dynamics is a special case). The second paper presents an implementation and application. The implementation is available as a set of Fortran subroutines that should be easy to integrate into any MD program (we used an old version of Gromos); write to me if you are interested. Please note that I didn't spend much effort to optimize the implementation. In my experience, constraint-type dynamics, in whatever way it is implemented, does not work well for significantly reduced coordinate sets, and is of little advantage for almost-complete coordinate sets, so I didn't want to invest any more effort. Another paper that could be of interest for you is L.M. Rice, A.T. Br"unger Torsion Angle Dynamics: Reduced Variable Conformational Sampling Enhances Crystallographic Structure Refinement Proteins 19, 277 (1994) It describes protein dynamics in phi-psi space (i.e. a subset of torsional angle space) for use in structure refinement, i.e. simulated annealing. For that application, the correctness of the dynamics is unimportant, so rather drastic constraints can be useful. But then you might be better off with some Monte-Carlo method if you don't care about dynamics. I suppose this method is implemented in some version of XPlor. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- ////////////////////////////////////////////////////////////////////////////// // Answer ///////////////////////////////////////////////////////////////////////////// Try the following programs: http://www.scsb.utmb.edu/fantom/ http://dasher.wustl.edu/tinker/ This is a good software list: http://antas.agraria.uniss.it/software.html hope this helps, --------------------------------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Institute of Parallel and Distributed High-Performance Systems (IPVR) University of Stuttgart Breitwiesenstrasse 20-22 D-70565 Stuttgart (Germany) email: Frank.Herrmann@informatik.uni-stuttgart.de http://www.informatik.uni-stuttgart.de/ipvr/bv/personen/herrmann.html --------------------------------------------------------------------- ------------------------------------------------------------------------------- Yongxing Liu, Graduate Student | E-Mail: yliu@wesleyan.edu Department of Chemistry | Tel.: 860-685-2777 Wesleyan University | Fax: 860-685-2211 Middletown CT 06457 | URL: http://ludwig.chem.wesleyan.edu/yliu ------------------------------------------------------------------------------- From goddette@tripos.com Thu Jul 2 15:02:03 1998 Received: from gatekeeper.tripos.com (gatekeeper.tripos.com [38.154.18.254]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA03870 Thu, 2 Jul 1998 15:01:59 -0400 (EDT) Received: (from uucp@localhost) by gatekeeper.tripos.com (SMI-8.6/8.6.12) id OAA14227 for ; Thu, 2 Jul 1998 14:02:29 -0500 Received: from unknown(38.154.18.101) by gatekeeper.tripos.com via smap (4.1) id xma014216; Thu, 2 Jul 98 14:02:24 -0500 Message-ID: <359BD9AA.C8CC663F@tripos.com> Date: Thu, 02 Jul 1998 14:04:10 -0500 From: Dean Goddette Reply-To: goddette@tripos.com Organization: Tripos, Inc. X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Meeting Announcement X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Midwest Molecular Modeling Meeting (M4) APPLICATIONS IN COMPUTER-AIDED DRUG DESIGN July 14, 1998 Indianapolis, Indiana It is my pleasure to announce the Midwest Molecular Modeling Meeting entitled "Applications in Computer-Aided Drug Design", a one-day scientific symposium hosted by Tripos, Inc. to be held on July 14, 1998 in Indianapolis, Indiana. The theme for the meeting is the application of computational chemistry in pharmaceutical/agrochemical research. We have an exciting slate of speakers who will cover a broad range of topics including QSAR, structure-based drug design and combinatorial chemistry. SPEAKER LIST ============ Dr. Robert Pearlman, University of Texas, Austin -- Recent Advances In Chemical Diversity, Library Design And Virtual High Throughput Screening. Dan Ortwine, Parke Davis -- Structure Based Design Of Metric Metalloproteinase Inhibitors, What Have The Structures Taught Us? Dr. Salvatore Profeta, Monsanto -- Combinatorial Library Design and Optimization Utilizing QSAR and QSRA(Quantitative Structure-Reactivity Analysis) Techniques. Dr. Jon Erickson, Dow Agrosciences -- Approaches To Molecular Alignment For CoMFA Dr. James Metz, Lilly Research Laboratories -- Insights and Computational Approaches to the Problem of Drug Permeability To Be Announced Dr. Bobby Barnett, Procter and Gamble Pharmaceuticals === The meeting will take place at the Hyatt Regency, downtown Indianapolis. Registration will begin at 8AM along with breakfast. Talks will begin at 9AM, ending at 3PM with a break for lunch. Registration for the meeting is $80 commercial, $40 academic. For more information or registration information, please see our web site at or contact Jamie Heritage at 1-800-323-2960. -- Dean Goddette, Ph.D. email: goddette@tripos.com Central US & Canada phone: 314-647-1099 x3386 Tripos, Inc. fax: 314-647-9241 1699 South Hanley Road WWW: http://www.tripos.com St. Louis, MO 63144 USA From ccl@www.ccl.net Fri Jul 3 11:33:11 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA11518 Fri, 3 Jul 1998 11:33:10 -0400 (EDT) Received: from mailsorter-105.bryant.webtv.net (mailsorter-105.iap.bryant.webtv.net [207.79.35.95]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA19438 for ; Fri, 3 Jul 1998 11:33:10 -0400 (EDT) Received: from mailtod-101.iap.bryant.webtv.net (mailtod-101.iap.bryant.webtv.net [207.79.35.81]) by mailsorter-105.bryant.webtv.net (8.8.8/ms.gso.08Dec97) with ESMTP id IAA02181; Fri, 3 Jul 1998 08:33:10 -0700 (PDT) Received: (from production@localhost) by mailtod-101.iap.bryant.webtv.net (8.8.8/mt.gso.26Feb98) id IAA09362; Fri, 3 Jul 1998 08:33:10 -0700 (PDT) X-WebTV-Signature: 1 ETAtAhQuR3Pwh04gU2alBhRKndowIVJEigIVAJzCFyup3AzTSFUi8LzbRnlzTDAj From: SCIENCELINK@webtv.net (BARRY BITTINGER SR.) Date: Fri, 3 Jul 1998 11:33:10 -0400 (EDT) To: Chemistry@ccl.net Subject: Solid Rocket Fuel Emissions Message-ID: <27503-359CF9B6-106@mailtod-101.iap.bryant.webtv.net> Content-Type: Text/Plain; Charset=US-ASCII Content-Transfer-Encoding: 7Bit MIME-Version: 1.0 (WebTV) I respectfully request your input into my concerns about what chemicals are emitted in the smoke of thermal chemical fuel, specifically solid rocket fuel, when all these chemicals are burned together at one time? atomized aluminm powder (fuel) 16% ammonium perchlorate (oxidizer) 69.83% iron oxide powder (catalyst) 17% (varies) polybutadiene acrylic acid acrylonitrite (binder) 12% AKA carbonated polyester epoxy curing agent 2% Thank you very much. I would appreciate feedback. From Barry W. Bittinger Sr. SCIENCELINK@webtv.net From d3e102@emsl.pnl.gov Mon Jul 6 15:59:02 1998 Received: from pnl.gov (relay.pnl.gov [130.20.128.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA12142 Mon, 6 Jul 1998 15:59:01 -0400 (EDT) From: d3e102@emsl.pnl.gov Received: from odyssey.emsl.pnl.gov by pnl.gov (PMDF V5.1-10 #21283) with ESMTP id <01IZ2XJC5C1C8X1X51@pnl.gov> for chemistry@www.ccl.net; Mon, 6 Jul 1998 12:58:28 PDT Received: from ames.emsl.pnl.gov (ames.emsl.pnl.gov [198.128.80.135]) by odyssey.emsl.pnl.gov (8.8.5/8.8.5) with ESMTP id MAA19252 for ; Mon, 06 Jul 1998 12:58:27 -0700 (PDT) Received: (from d3e102@localhost) by ames.emsl.pnl.gov (8.8.5/8.8.5) id MAA07638 for chemistry@www.ccl.net; Mon, 06 Jul 1998 12:58:27 -0700 (PDT) Date: Mon, 06 Jul 1998 12:58:27 -0700 Subject: BSSE and (H2O)2 To: chemistry@www.ccl.net Message-id: <9807061258.ZM7636@ames.emsl.pnl.gov> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.0 06sep94) Content-type: text/plain; charset=us-ascii Over the past several weeks there have been several messages posted to the CCL concerning basis set superposition error and the water dimer. Here is an admittedly selective list of just some of the calculations dealing with the water dimer. This system has been examined by a large number of researchers. ----------------------------------------------------------------------------- Water Dimer Interaction Energies (kcal/mol) Basis Method DeltaE CP Reference aug-cc-pVQZ MP2(FC) -5.05 N D. Feller, JCP 96, 6104 MP2(FC) -4.81 Y (1992). (See Note 1) Est. CBS MP2(FC) -4.95 +/- 0.05 NA R12-MP2 -4.94 NA W. Klopper, et al. JCP, 103, 1085 (1995). aug-cc-pV5Z MP2(FC) -4.98 N M.W. Feyereisen et al. JPC Est. CBS MP2(FC) -4.9 +/- 0.1 NA 100, 2993 (1996). Est. CBS MP2 -4.95 +/- 0.1 NA Est. CBS FCI -5.0 +/- 0.1 NA (see Note 2) 20s15p11d9f7g4h2i1k MP2(FC) -4.92 N M. Schutz et al. JCP, 107, MP2(FC) -4.88 Y 4597 (1997). Est. CBS MP2 -4.94 +/- 0.02 NA (see Note 3) aug-cc-pV5Z MP2(FC) -4.98 N A. Halkier, et al. TCA, 97, daug-cc-pVQZ MP2(FC) -5.10 N 150 (1997). MP2(FC) -4.81 Y Est. CBS MP2(FC) -4.91 +/- 0.07 NA aug-cc-pVQZ CCSD(T)(FC) -5.05 N Est. CBS CCSD(T)(FC) -4.96 +/- 0.07 NA CP: N=No, Y=Yes/ NA=Not Applicable Note 1: The aug-cc-pVQZ binding energy was estimated by assuming the contributions of the diffuse f and g functions on oxygen were additive. Note 2: The full CI estimate includes the effects of geometry relaxation, core/valence corrections and higher order correlation recovery. Note 3: The (20s15p11d9f7g4h2i1k) oxygen basis set of Schutz et al. was uncontracted. It was used with an 11s5p4d3f2g1h hydrogen basis set for a total of 1046 functions in the water dimer. These authors state that their core/valence correction was only 0.04 kcal/mol, whereas they claim that Feyereisen et al. recommended a value of 0.09 kcal/mol. But in the abstract to the work of Feyereisen et al. they clearly state that CV effects increase the binding energy by ~0.05 kcal/mol. -- David Feller | Mail Stop K1-96 Environmental Molecular Sciences Laboratory | 906 Battelle Blvd Battelle Pacific Northwest National Lab | Richland, WA 99352 | e-mail:d3e102@emsl.pnl.gov | Fax: (509)-375-6631