From chemistry-request@server.ccl.net Tue Aug 7 05:00:15 2001 Received: from gatekeeper.bnfl.co.uk ([193.35.7.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7790Ev22614 for ; Tue, 7 Aug 2001 05:00:15 -0400 Received: by gatekeeper.bnfl.co.uk; id JAA02077; Tue, 7 Aug 2001 09:57:59 +0100 (BST) From: Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma001777; Tue, 7 Aug 01 09:56:48 +0100 Received: from ASN027.bnfl.com (unverified) by ant008.spr.bnfl.com (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Tue, 7 Aug 2001 09:38:06 +0100 Received: from BNotesMTA1.sell.bnfl.com ([10.30.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id JAA07333 for ; Tue, 7 Aug 2001 09:43:48 +0100 (BST) Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.7 (934.1 12-30-1999)) id 00256AA1.0035D094 ; Tue, 7 Aug 2001 09:47:48 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-ID: <00256AA1.0035CF5C.00@BNotesMTA1.sell.bnfl.com> Date: Tue, 7 Aug 2001 09:47:58 +0000 Subject: MOPAC2000 3D periodic file Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Hi there, am having a little trouble in getting MOPAC2000 to work with a 3D periodic model and I was wondering if someone on this list had used MOPAC2000 for any system of this sort and would be willing to send me an input file so that I can compare it to what I have been using. The models I am trying to run are extended periodic models of graphite. If anyone has an input file for a simple extended periodic input file (no symmetry assumed) that works in MOPAC2000 then maybe I can guess where I am going wrong! The systems I am trying to optimise are (pxqxr) models reduced to a single unit cell with P1 symmetry (p,q,r are all integers). I have tried using the MAKPOL facility with MOPAC2000 but it gives the same input file for MOPAC2000 that I am already using, constructing such cells in MOPAC2000 does not appear to be difficult at first sight for such models. Incidentally the problem is that some of the atoms in the periodic model are wandering a long way from their preferred positions and the structure is buckling badly from the planar sheet of graphite atoms that we all are familiar with. If there is any other theoretical reason why graphite should do this under AM1 or PM3 semi-empirical then this would also be gratefully received. Scott Owens slo1@bnfl.com From chemistry-request@server.ccl.net Tue Aug 7 08:48:07 2001 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f77Cm7v25995 for ; Tue, 7 Aug 2001 08:48:07 -0400 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Tue, 7 Aug 2001 13:48:05 +0100 Sender: mb@ucl.ac.uk Message-ID: <3B6FE2D2.34C296F1@ucl.ac.uk> Date: Tue, 07 Aug 2001 13:45:06 +0100 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Thomas Heine CC: chemistry@ccl.net Subject: Re: CCL:beyond Verlet's algorithm References: <01080610031300.07943@lcta1> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thomas Heine wrote: > > Dear CCLers, > > many MD codes use Verlet's algorithm to obtain trajectories in MD > simulations. This algorithm is very compact and optimized for > - minimal storage of information > - minimal number of operations in the integration process > to advance coordinates (and velocities) with time. > > Let's assume that the computing time needed to get new coordinates R(t+ delta > t) is negligible to the time spent for calculating energy and forces. > > My question is whether there is a more sophisticated algorithm around, which > integrates with an as large as possible delta t (determined with some > theshold), which uses coordinates, velocities and accelerations of N previous > iterations? There's, e.g., different kinds of "predictor corrector" and "Runge-Kutta" algorithms (see "Numerical Recipies", W. H. Press) however, low memory consumption and fast execution are not the only advantages of the Verlet (or the equivalent velocity Verlet and leap frog) algorithm. It is also a so called symplectic/time-reversible algorithm with the important consequence that the total energy is well conserverd in the course of an MD simulation. When performing longish MD runs with higher order algorithms you usually have to use a quite small time step to avoid heating up of the the system (unless of course you use a thermostate, but it might be physically rather questionable to use a thermostate for such a purpose). I believe that, unless you have really good reasons for using them, the effort involved in implementing such higher order algorithms wouldn't pay out. regards mic =================================================================== What I like most about myself is that I'm so understanding when I mess things up. ------------------------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk http://www.ucl.ac.uk/~uccambr/ ------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Aug 7 10:23:51 2001 Received: from ne059.cm.utexas.edu ([146.6.145.59]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f77ENpv28651 for ; Tue, 7 Aug 2001 10:23:51 -0400 Received: from eeyore.cm.utexas.edu (ne057.cm.utexas.edu [146.6.145.57]) by ne059.cm.utexas.edu (8.10.2/8.10.2) with ESMTP id f77E5D610289; Tue, 7 Aug 2001 09:05:13 -0500 Message-ID: <3B6FF885.52671B86@eeyore.cm.utexas.edu> Date: Tue, 07 Aug 2001 09:17:41 -0500 From: "Isaac B. Bersuker" Organization: The University of Texas at Austin X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Mike Peleah CC: chemistry@ccl.net Subject: Re: CCL:small molecule activation References: <1692991567.20010806132304@yahoo.com> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Please, have a look on Section 11.2 in my latest book on Electronic Structure and Properties..., Wiley, NY, 1996, pp 578-603, especially pp 586-600, maybe you will find some of the information you are looking for. Isaac Bersuker Mike Peleah wrote: > Dear chemistry, > > Could anybody give me a reference on recent paper(s) (preferably > review) on quantum-chemical investigation of small molecule > activation? > > Thanks. I'll summarize answers. > > Best regards, > Mike mailto:MikePeleah@yahoo.com > > -= 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 -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712 Phone: (512) 471-4671 Fax: (512) 471-8696 E-mail: bersuker@eeyore.cm.utexas.edu From chemistry-request@server.ccl.net Tue Aug 7 10:55:27 2001 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f77EtQv29188 for ; Tue, 7 Aug 2001 10:55:26 -0400 Received: from chemie.uni-erlangen.de (indigo11.chemie.uni-erlangen.de [131.188.128.69]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id QAA09681 for ; Tue, 7 Aug 2001 16:55:26 +0200 (MET DST) Sender: Harald.Lanig@Organik.Uni-Erlangen.DE Message-ID: <3B700189.A8F71534@chemie.uni-erlangen.de> Date: Tue, 07 Aug 2001 16:56:09 +0200 From: Harald Lanig Organization: Computer-Chemie-Centrum Uni Erlangen/Nbg X-Mailer: Mozilla 4.08 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Model(l)ing 2001 in Erlangen/Germany: Bursaries and Awards available! Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit Dear colleagues, The complete program for Model(l)ing 2001 (16 - 21 September 2001 in Erlangen, Germany) is now available on the website http://www.chemie.uni-erlangen.de/model2001/. A few places for participants are still available at the conference. We are also pleased to announce the following awards for the conference: Accelrys Awards We are pleased to announce two Accelrys Awards of USD 1000 each to support participants to Model(l)ing 2001 from less developed countries. Applications (with CV in English and including a poster abstract) should be sent by email to model01@chemie.uni-erlangen.de. Closing date for applications is August 31, 2001. Successful applicants will be informed by email immediately after this date. MGMS Bursaries The Molecular Graphics and Modelling Society is offering Bursaries to support graduate students attending Model(l)ing 2001. Eight bursaries, each of Euro 1000, will be awarded to graduate students attending the conference and presenting a poster. Applications (with CV in English and including a poster abstract) should be sent by email to model01@chemie.uni-erlangen.de. Closing date for applications is August 31, 2001. Successful applicants will be informed by email immediately after this date. Accelrys Poster Prizes A total of eight poster prizes will be awarded, a cash Prize of BP ?100 and two of BP 50 (sponsored by the MGMS) and five book prizes (Pharmacophore Perception, Development, and Use in Drug Design; Ed. by O. F. Guner) sponsored by Accelrys. The deadline for poster submission has been extended to August 31. NEW!!! The conference dinner will take place in the railway museum in Nuremberg, the site of Germany's first railway. We are looking forward to see you in Erlangen! Harald Lanig and Tim Clark -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Lehrstuhl fuer Schuhstrasse 19 Pharmazeutische Chemie D-91052 Erlangen, Germany oder Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 Mailto:lanig@chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/clark/lanig ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Aug 7 08:45:12 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f77CjBv25937 for ; Tue, 7 Aug 2001 08:45:11 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id OAA23121 ; Tue, 7 Aug 2001 14:44:59 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id OAA02595; Tue, 7 Aug 2001 14:45:09 +0200 Date: Tue, 7 Aug 2001 14:45:09 +0200 Message-Id: <200108071245.OAA02595@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: thomas.heine@chiphy.unige.ch CC: chemistry@ccl.net In-reply-to: <01080610031300.07943@lcta1> (message from Thomas Heine on Mon, 06 Aug 2001 10:03:13 +0200) Subject: Re: CCL:beyond Verlet's algorithm References: <01080610031300.07943@lcta1> > My question is whether there is a more sophisticated algorithm > around, which integrates with an as large as possible delta t > (determined with some theshold), which uses coordinates, velocities > and accelerations of N previous iterations? Various integrators known from numerical analysis have been tried, but although some of them have a better accuracy on short time scales, they all tend to be less stable on long time scales. A lot of literature exists on that topic, the keyword to look for is "symplectic integrators". There are other symplectic integrators than the Verlet algorithm, and some of them permit larger time steps (e.g. multiple time step integrators), but not in the way you describe, and not without "help" from the energy evaluation. Note also that MD integration is more of a black art than science. Most simulations are performed with time steps that are much too large compared to the frequency of the system, using standard criteria from the theory of differential equations. And indeed such time steps do not give good results for e.g. single molecules, a large system is required to make them acceptable, probably due to error cancellation. Moreover, it is well known (but rarely discussed) that of all the theoretically conserved quantities, only the total energy is preserved reasonably well in MD. Momentum and (for non-periodic systems) angular momentum are usually "reset" periodically to prevent the accumulation of deviations. A much smaller time step will give good conservation of all these quantities, but is not used because of excessive CPU times. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Aug 7 14:48:17 2001 Received: from mail.london-1.starlabs.net ([212.125.75.12]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f77ImGv03842 for ; Tue, 7 Aug 2001 14:48:16 -0400 X-VirusChecked: Checked Received: (qmail 9678 invoked from network); 7 Aug 2001 18:44:11 -0000 Received: from wesson.apci.com (HELO crypto.apci.com) (204.27.156.141) by server-19.tower-4.starlabs.net with SMTP; 7 Aug 2001 18:44:11 -0000 Received: from 144.249.168.155 by crypto.apci.com with SMTP (Tumbleweed MMS SMTP Relay (MMS v4.7)); Tue, 07 Aug 2001 14:48:15 -0400 X-Server-Uuid: 0a59d787-ec29-11d2-907b-0008c7f41790 Received: from naex000b.apci.com (naex000b.apci.com [144.249.178.60]) by relay.apci.com (8.8.5/8.8.5) with ESMTP id OAA25296 for ; Tue, 7 Aug 2001 14:48:15 -0400 (EDT) Received: by naex000b.apci.com with Internet Mail Service (5.5.2653.19) id ; Tue, 7 Aug 2001 14:48:15 -0400 Message-ID: From: "Peterson,Brian K." To: chemistry@ccl.net Subject: VASP trajectory to Cerius input Date: Tue, 7 Aug 2001 14:48:14 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 176EE865690503-01-01 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Hello. Does anyone have a routine for converting VASP trajectory files to something that can be read by Cerius2? A .his file is preferred. Thanks very much. We will summarize for the list. Dr. Brian K. Peterson Air Products and Chemicals, Inc. 7201 Hamilton Boulevard phone: 610-481-3850 Allentown, PA 18195-1501 fax: 610-706-7672 USA + From chemistry-request@server.ccl.net Tue Aug 7 15:49:52 2001 Received: from onsager.cop.uop.edu ([138.9.240.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f77Jnpv04969 for ; Tue, 7 Aug 2001 15:49:52 -0400 Received: (from mccallum@localhost) by onsager.cop.uop.edu (8.9.3/8.9.3) id MAA00744; Tue, 7 Aug 2001 12:51:25 -0700 Date: Tue, 7 Aug 2001 12:51:25 -0700 From: "C. Michael McCallum" To: Sidney Ramos , CCL List Subject: Re: CCL:MPI libraries for Solaris Message-ID: <20010807125125.A730@onsager.cop.uop.edu> Reply-To: "C. Michael McCallum" References: <20010801144254.35959.qmail@web11907.mail.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2i In-Reply-To: <20010801144254.35959.qmail@web11907.mail.yahoo.com>; from magneticdolphin@yahoo.com on Wed, Aug 01, 2001 at 07:42:54AM -0700 * Sidney Ramos (magneticdolphin@yahoo.com) [010801 11:39]: > Dear CCLers and Dalton Users, > > I get the last Dalton 1.2 version and I wish I > compiled the parallel version in the Sun Entreprise(4 > nodes). Anybody knows where can I get MPI libraries > for Solaris? > Thanks for any help! > Best Regards, > Sun MPI should have come in your software bundle. If you can compile for parallel (mpcc or hpcc compiler(s)), you should have the MPI installed. If you don't, I'd talk to Sun. The Forte suite for MP machines is very reasonable for academics. That being said, I have had major problems with Sun's MPI under some specific applications (DL_POLY, for example). You may want to try the free MPI implementations someone else mentioned. Cheers, Mike McCallum -- C. Michael McCallum | "That may be one tough nut to crack, Associate Professor | but I am one determined Chemistry, UOP | little squirrel" mmccallum@uop.edu | (209) 946-2393 | fax (209) 946-2607 From chemistry-request@server.ccl.net Tue Aug 7 21:17:21 2001 Received: from relay2.softcomca.com ([168.144.1.68]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f781HKv09826 for ; Tue, 7 Aug 2001 21:17:20 -0400 Received: from m2w036 ([168.144.108.36]) by relay2.softcomca.com with Microsoft SMTPSVC(5.0.2195.3779); Tue, 7 Aug 2001 21:18:54 -0400 X-Originating-IP: 202.185.72.119 X-URL: http://www.mail2web.com/ Subject: Docking multiple ligands in one protein Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Tue, 7 Aug 2001 21:17:21 -0400 To: "chemistry@ccl.net" Reply-To: nepenthes@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-ID: X-OriginalArrivalTime: 08 Aug 2001 01:18:54.0223 (UTC) FILETIME=[16E619F0:01C11FA8] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id f781HLv09827 Dear All, I would like to post this question regarding docking. Has anybody used Autodock for docking more than one ligand to a protein? My protein has six binding sites and they all bind to the same ligand, hence six ligands. My question would be: 1)is it better to dock the ligands individually to their respective sites or dock them one after another in the binding sites? By docking one after another, meaning second ligand will be docked with the first ligand attached to it from the first docking on the first site. 2)If I dock the ligand one after another, I'm not sure what criteria I can use to choose the best docked conformation as sometimes the lowest energy docked does not give the best interactions as compared to the crystal structure. At the moment, I always choose the lowest docked conformations. The articles I have read concerns docking of one ligand to protein. I would be grateful for some advice or suggestions. Thank you very much in advance and I'll summarize the answers. Sincerely, Rowyna K. Institute of Biological Sciences, Kuala Lumpur -------------------------------------------------------------------- Mail2Web - Check your email from the web at http://www.mail2web.com/ .