From chemistry-request@www.ccl.net Mon Mar 8 04:42:04 1999 Received: from comsig.nibsc.ac.uk (comsig.nibsc.ac.uk [193.62.43.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA09944 Mon, 8 Mar 1999 04:41:59 -0500 (EST) Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by comsig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA17244 for ; Mon, 8 Mar 1999 09:40:42 GMT Message-ID: <36E39B31.5F5FECAB@nibsc.ac.uk> Date: Mon, 08 Mar 1999 09:41:05 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL:conformational search on ring systems Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL chemists On Tue, 2 Mar 1999, Tamas Gunda wrote: > > is anybody aware of a software package that has a conformational > > search tool applicable to ring-systems ? I'll address this in two parts 1) Code to measure ring conformation parameters. 2) Software to manipulate ring conformations interactively. 1) For six membered rings our Unix/X11 code called mdXvu is available from the Quantum Chemistry Program Exchange (QCPE) and one of its features is the measurement of the Cremer Pople ring puckering parameters. 2) The Biopolymer module of insightII (from MSI) has a nice tool for 'ring flapping' i.e. selecting two atoms in a ring and pivoting the intermediate ring atoms about the selected pair while maintaining the bond lengths and angles. This works for 5,6,7.... membered rings. Hope this helps. -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@www.ccl.net Mon Mar 8 09:56:34 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA12012 Mon, 8 Mar 1999 09:56:30 -0500 (EST) Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA11670 for ; Mon, 8 Mar 1999 15:54:17 +0100 (CET) Date: Mon, 8 Mar 1999 15:54:16 +0100 From: Christian Pilger To: chemistry@www.ccl.net Subject: estimation of binding constants (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, one week ago I posted a question concerning the estimation of binding constans: > I did some docking on an enzyme/ligand complex. Now I have the > problem of scoring the results i.e. prediction the binding constants for > different enzyme-ligand alignments. I'd like to receive some information > on this topic (molecular mechanics vs. quantum mechanics vs. empirical > scoring schmemes...). I got one answer: > From: Carlos Faerman > Check out the following publication and the free software that can be > obtained from the authors: > "SCORE: A new empirical method for estimating the binding affinity of a > protein-ligand complex" J. Mol. Model. (1998) 4, 379-394 > and one contact > e-mail address is : lai@ipc.pku.edu.cn Thank you very much. Regards, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Mar 8 11:29:13 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13339 Mon, 8 Mar 1999 11:29:12 -0500 (EST) Received: from istanbul.ks.uiuc.edu (istanbul.ks.uiuc.edu [130.126.120.95]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id KAA10393; Mon, 8 Mar 1999 10:30:45 -0600 (CST) Received: from localhost (jim@localhost) by istanbul.ks.uiuc.edu (8.8.7/8.6.9) with ESMTPid KAA25292; Mon, 8 Mar 1999 10:29:08 -0600 X-Authentication-Warning: istanbul.ks.uiuc.edu: jim owned process doing -bs Date: Mon, 8 Mar 1999 10:29:08 -0600 (EST) From: Jim Phillips X-Sender: jim@istanbul To: takanori.kanazawa@pharma.Novartis.com cc: chemistry@www.ccl.net, namd@ks.uiuc.edu Subject: Re: CCL:help:NAMD2 In-Reply-To: <4925672A.000D2CEE.00@nts1.novartis.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I'm one of the NAMD2 developers. That error message, which I admit isn't terribly helpful, arises from a (generous but unnecessary) hard limit in the code. This line should shed some light on the situation: Info: PATCH GRID IS 69 (PERIODIC) BY 69 (PERIODIC) BY 69 (PERIODIC) Your 1000 atom system is occupying a cell which is 69 *patches* in each dimension. For any reasonable cutoff a patch is at least 10 A, which means your cell is 700 A on a side. I would suggest either not using periodic boundaries or using a smaller cell. In any case, NAMD's spatial decomposition scheme is not efficient for sparse (gas-phase) problems. This simulation appears to be a small molecule in some atomic solvent. If this is really what you want, you will see much better performance if you adjust the patch size to about 1/5 or 1/10 of your cell size using the margin parameter. As I said, NAMD is targetted at large liquid phase simulations so your performance on this small gas will be quite poor. -Jim On Thu, 4 Mar 1999 takanori.kanazawa@pharma.Novartis.com wrote: > > > Dear CCLers, > > Could someone help me to solve a problem with a MD simulation using > namd2. > > I downloaded namd2.0b3(binary) from the namd homepage and installed > on my SGI machine(octance R10000 250MHz, 2cpu, IRIX6.4). > When I ran a MD simulation with a periodic boundary condition, the job > stopped > with the following messages. > > ..... > Info: **************************** > Info: STRUCTURE SUMMARY: > Info: 1012 ATOMS > Info: 11 BONDS > Info: 18 ANGLES > Info: 16 DIHEDRALS > Info: 2 IMPROPERS > Info: 0 EXCLUSIONS > Info: 3033 DEGREES OF FREEDOM > Info: 1005 HYDROGEN GROUPS > Info: ***************************** > Info: Entering startup phase 0 > Info: Entering startup phase 1 > Info: Entering startup phase 2 > Info: Entering startup phase 3 > Info: PATCH GRID IS 69 (PERIODIC) BY 69 (PERIODIC) BY 69 (PERIODIC) > Info: REMOVING COM VELOCITY ( -0.1068, 0.0186864, -0.00757281) > Info: 1012 atoms assigned to node 0 > ID's not allocated in ComputeMap::storeCompute(). > ############### END of the log-file ############### > > The sample job attached to the program(MD of alanine oligopeptide) runs > without any problem. > > Any comments or suggestions are appreciated. > > > Thanks in advance, > > Takanori Kanazawa > > *************************************************************** > Takanori Kanazawa > E-mail : takanori.kanazawa@pharma.novartis.com > > Drug Discovery Group / CAMM > Takarazuka Research Institute > Novartis Pharma K.K. > 10-66 Miyuki-cho, Takarazuka, Hyogo 665 > JAPAN > *************************************************************** > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From chemistry-request@www.ccl.net Mon Mar 8 11:41:27 1999 Received: from rztsun.rz.tu-harburg.de (rztsun.rz.tu-harburg.de [134.28.200.14]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13422 Mon, 8 Mar 1999 11:41:23 -0500 (EST) Received: from pluto.vt4.tu-harburg.de (vt4xg@pluto.vt4.tu-harburg.de [134.28.43.135]) by rztsun.rz.tu-harburg.de (8.9.0/8.8.8) with ESMTP id RAA16994 for ; Mon, 8 Mar 1999 17:41:11 +0100 (MET) Message-ID: X-Mailer: XFMail 1.2 [p0] on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 Date: Mon, 08 Mar 1999 17:40:55 +0100 (MET) Organization: TU Hamburg-Harburg Sender: vt4xg@pluto.vt4.tu-harburg.de From: Xiangyun Guo To: chemistry@www.ccl.net Subject: Fracton dimeension of "menger Sponge " surface Hi, Dear friends For homo-bimolecular reactions over fractal substrates A + A --- products according to the proposal by Kopelman et al. the reaction order should be X = 1 + 2/Ds where Ds is the fracton dimension. I would like to know the Ds value of the surface of the three-dimensional "Menger Sponge", could you tell me ? Best Regards Xiangyun GUO ---------------------------------- E-Mail: Xiangyun Guo Date: 08-Mar-99 Time: 17:39:10 This message was sent by XFMail ---------------------------------- From chemistry-request@www.ccl.net Mon Mar 8 16:54:46 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA24486 Mon, 8 Mar 1999 16:54:42 -0500 (EST) Received: from ligquim ([143.107.194.89]) by swan2.uspnet.usp.br (8.9.1a/8.9.1) with SMTP id SAA20221 for ; Mon, 8 Mar 1999 18:51:31 -0300 (EST) Message-ID: <000701be69ae$3558f180$0100005a@ligquim.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: "CCL mail list" Subject: G: ONIOM using ECP Date: Mon, 8 Mar 1999 18:54:14 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 7bit Dear Netters, I am trying to run a metal complex job using ONIOM. In the higher layer I am using LSDA/LANL2DZ and in the lower HF/3-21G. The job bumps in the beginning and presents the following: ================================ Leave Link 202 at 18:18:19 on 03/08/99 , MaxMem= 6291456 cpu: 0.8 (Enter /usr/local/g98/l120.exe) ONIOM: generating new system at layer 2 ONIOM: saving gridpoint 9 Leave Link 120 at 18:18:20 on 03/08/99 , MaxMem= 6291456 cpu: 0.0 (Enter /usr/local/g98/l301.exe) Standard basis: 3-21G (6D, 7F) ============================================================================ ======================================================= PSEUDOPOTENTIAL PARAMETERS ============================================================================ ======================================================= CENTER ATOMIC VALENCE ANGULAR POWER COORDINATES NUMBER NUMBER ELECTRONS MOMENTUM OF R EXPONENT COEFFICIENT X Y Z ============================================================================ ======================================================= EOF while reading ECP pointer card. Error termination via Lnk1e in /usr/local/g98/l301.exe. =========================================== Thanks a lot, Sergio ============================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo fax: +55-16-633-81-51 e-mail: segalemb@usp.br ===============================================