From chemistry-request@server.ccl.net Sat Nov 2 08:43:53 2002 Received: from Mailer.Uni-Marburg.DE ([137.248.1.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA2Dhqf14969 for ; Sat, 2 Nov 2002 08:43:52 -0500 Received: from mailer.uni-marburg.de (pc16187.Pharmazie.Uni-Marburg.DE [192.168.161.187]) by Mailer.Uni-Marburg.DE (8.11.2/8.11.2) with ESMTP id gA2DdwZ46180 for ; Sat, 2 Nov 2002 14:39:58 +0100 Sender: sotriff@Staff.Uni-Marburg.DE Message-ID: <3DC3D5AA.5F06F3BF@mailer.uni-marburg.de> Date: Sat, 02 Nov 2002 14:39:54 +0100 From: Christoph Sotriffer X-Mailer: Mozilla 4.78 [de] (X11; U; Linux 2.4.10-64GB-SMP i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Workshop: New Approaches in Drug Design Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-MailScanner: Found to be clean The "3rd Intl. Workshop on New Approaches in Drug Design & Discovery" will be held in Schloss Rauischholzhausen, near Marburg, Germany, > from Monday, March 24, to Thursday, March 27, 2003. The title of the workshop is: From High-Throughput to High-Output: Can 'Omics' Assist Computational Drug Design? Any further information regarding the program and the registration procedure, as well as accommodation and location can be found at the following website: http://www.agklebe.de/workshop2003 Deadline for registration is Dec-31-2002, but earlier application is highly recommended since no more than 90 participants can be accepted. Best regards, Christoph Sotriffer --------------------------- Christoph Sotriffer Dept. of Pharm. Chemistry Philipps-University Marburg --------------------------- From chemistry-request@server.ccl.net Sat Nov 2 21:24:35 2002 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA32OXw12470 for ; Sat, 2 Nov 2002 21:24:34 -0500 Received: from PC12 (unknown [202.127.19.236]) by smtp01.sohu.com (Postfix) with ESMTP id 9992753593; Sun, 3 Nov 2002 09:59:56 +0800 (CST) Date: Sun, 3 Nov 2002 10:26:11 +0800 From: "zgleo" To: Zengjian Hu Cc: "CHEMISTRY@ccl.net" Subject: Re: Re: CCL:Re: Sybyl question X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Message-Id: <20021103015956.9992753593@smtp01.sohu.com> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gA32OZw12473 Dear Zengjian Hu, Thank you for your help,but maybe I didn't explain my question clearly.I find in autodock you needn't define the grid box by hand,and moreover,you also needn't define the analogous file like "exclude.pdb" used to define the location and scale of the box in dock4.0. Here the grid box is defined in the macro.gpf by the command "mkgpf3 ligand.pdbq macro.pdbqs",It seems that the gird center generated automatically correlates only with the location of the ligand.(You can try to move the ligand to a position far away from the receptor and proceed autodock from beginning,then read "macro.mol2","ligand.mol2" and "macro.gpf.pdb" into sybyl,you will find the box is overlapped by ligand,not receptor) So I think it's necessary to move the ligand into pocket before doing autodock,because if you have done this,you needn't modify the grid center in the grid parameter file "macro.gpf" during the process of autodock.It's important for doing autodock in a batch command file. Finally,My boss is Jianghualiang. Best Regards! --------------------- Liu Zhi-Guo Ph.D candidate Drug Design & Discovery Center Shanghai Institute of Materia Medica Shanghai,in China ======= 2002-11-02 12:52:00 Zengjian Hu wrote======= >Yes. Any docking program can put the ligand(s) >into the active site automatically. And it should >be. Just be careful to define the box. > > >By the way, who is your boss? > >Regards, > >Hu >---------------------------------------------- >Zengjian Hu, Ph. D. >Research Investigator >University of Michigan >1150 W. Medical Center Drive >2423 Med. Sci I >Ann Arbor, MI 48109-0934 >Ph# 734-764-2537 >Fax# 734-764-2532 >E-mail: huzengjian@hotmail.com >---------------------------------------------- > > > > > >>From: "zgleo" >>To: Zengjian Hu >>CC: "CHEMISTRY@ccl.net" >>Subject: CCL:Re: Sybyl question >>Date: Fri, 1 Nov 2002 22:31:10 +0800 >> >>Dear Zengjian Hu, >> >> Thank you for your help.You said I needn't put the ligand into the active >>site,did you mean >> the autodock will find the active site or the pocket >>automatically?Expecting your reply... >> >> >> Best regards! >>ˇˇzgleo >>ˇˇzgliu@sohu.com >>ˇˇ2002-11-01 >> >>======= 2002-11-01 14:19:00 zgleo wrote======= >> >> >Hi, >> > >> >If you just prepare the ligands for Autodock, you >> >don't need to put the ligand into the active site >> >of the receptor. Anywhere is OK. >> > >> >Best, >> > >> >Hu >> > >> >---------------------------------------------- >> >Zengjian Hu, Ph. D. >> >Research Investigator >> >University of Michigan >> >1150 W. Medical Center Drive >> >2423 Med. Sci I >> >Ann Arbor, MI 48109-0934 >> >Ph# 734-764-2537 >> >Fax# 734-764-2532 >> >E-mail: huzengjian@hotmail.com >> >---------------------------------------------- >> > >> > >> > >> > >> > >> >>From: "zgleo" >> >>To: "CHEMISTRY@ccl.net" >> >>Subject: CCL:Sybyl question >> >>Date: Fri, 1 Nov 2002 15:46:39 +0800 >> >> >> >>Dear CCLers, >> >> I find a strange problem when I use sybyl. >> >> I plan to prepare some ligands for autodock. >> >> The first thing I have to do is to move these ligands to the pocket >>area >> >>of the receptor. >> >> So I read the receptor molecule and ligand molecule into D1 and >> >>D2,respectively. >> >> Then I move the ligand to the pocket area by focusing mouse on D2,and >>then >> >>save it as >> >> "ligand.mol2"(Didn't freeze view). >> >> After this,I zap the D2 and read "ligand.mol2" into D2. >> >> It looks that everything is OK----the ligand molecule is exactly in the >> >>pocket. >> >> Unfortunately,when I zap everything and read "ligand.mol2" into sybyl >> >>firstly and receptor >> >> file into sybyl subsequently,I find the ligand is located far away from >> >>the receptor. >> >> Then I change the order again----that is reading the receptor first and >> >>the ligand second,to >> >> my surprise,the ligand is located in the pocket area again. >> >> I'm completely confused by it. >> >> Does anybody know why? >> >> Thanks. >> >> >> >> >> >>Best Regard! >> >>zgleo >> >>zgliu@sohu.com >> >>2002-11-01 >> >><< fox.gif >> >> > >> > >> >_________________________________________________________________ >> >Choose an Internet access plan right for you -- try MSN! >> >http://resourcecenter.msn.com/access/plans/default.asp >> >>= = = = = = = = = = = = = = = = = = = = >> >> >> >><< fox.GIF >> > > >_________________________________________________________________ >Unlimited Internet access for only $21.95/month.  Try MSN! >http://resourcecenter.msn.com/access/plans/2monthsfree.asp = = = = = = = = = = = = = = = = = = = = From chemistry-request@server.ccl.net Sun Nov 3 05:01:00 2002 Received: from dux.ru ([193.125.210.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA3A0xw23585 for ; Sun, 3 Nov 2002 05:01:00 -0500 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id gA3A7Rd1008122 for ; Sun, 3 Nov 2002 13:07:27 +0300 (MSK) (envelope-from dima@xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id gA3A7QHX008121 for chemistry@ccl.net; Sun, 3 Nov 2002 13:07:27 +0300 (MSK) (envelope-from dima@xenon.spb.ru) Received: from goblin (goblin [192.168.3.2]) by shadow (8.9.3/8.9.3/Debian 8.9.3-21) with SMTP id MAA29537 for ; Sun, 3 Nov 2002 12:58:33 +0300 Message-ID: <017701c2831f$9d4513d0$0203a8c0@goblin> From: "Dmitry Rozmanov" To: "CCL" References: <010d01c282cd$3fc9c6d0$0203a8c0@goblin> <97523713.20021103092129@bancorp.ru> Subject: Re: CCL:NWChem Date: Sun, 3 Nov 2002 12:58:52 +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 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Hi Gregory. Thank you for so complete replay. Then I'll stay with Gamess for a while ;). Regards. ---Dmitry. ----- Original Message ----- From: "Gregory Shamov" To: "Dmitry Rozmanov" Cc: "CCL" Sent: Sunday, November 03, 2002 9:21 AM Subject: Re: CCL:NWChem > Hello Dmitry, > > Sunday, November 3, 2002, 3:09:16 AM, you wrote: > > DR> Hi. > > DR> Does anybody use NVChem? > > I have tryed to use NWChem 4.0 and 4.01. > > DR> Does it have any advantages over Gamess-US? > > NO. > > The main advantage of Gamess (Gaussian, Jaguar, Qchem, ...) over > NWChem is that Gamess, in general, is stable, and NWChem, in general, > is not. > > And there are some minor disadvantages of NWChem. First, it slow. Very > slow. At single CPU it is about 2-4 times slower than Gamess. The > NWChem team says it is because NWChem is designed to be very > scalable code to use on hundreds and thousands CPUs. I believe it is > true, but for commonly used small clusters (8-16 CPUs) Gamess > outperforms NWChem. > > Moreover, NWChem (at least in some cases) running on the small cluster > (say, 8 CPUs) gives no normal speedup painting! I.e., wall times for > the same task are not smoothly decreasing with increasing CPU number, > but are changing randomly. Perhaps in the case on 1000 CPUs cluster > +\- 8 CPUs means nothing, aha, aha, but for small cluster every CPU > means a lot. :-) The same task calculated with Gamess on the same > cluster scales properly. > > There are a lot of methods implemented in NWChem: DFT, CCSD, CPMD, > classical MD, etc. But DFT (both grid-based and grid-free) and CCSD > methods are implemented in the latest versions of Gamess too, it is > possible to integrate Tinker with Gamess to do QM\MM and MD > calculations, and there is standalone free and cool CPMD program. > > So i think you better use these codes unless you have 1000CPUs > cluster. > > -- > Best regards, > Gregory Shamov mailto:gas5x@bancorp.ru From chemistry-request@server.ccl.net Sun Nov 3 05:10:55 2002 Received: from typhoeus.chem.york.ac.uk ([144.32.72.225]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA3AAsw23746 for ; Sun, 3 Nov 2002 05:10:54 -0500 Received: from ysbl.york.ac.uk (onion [144.32.72.165]) by typhoeus.chem.york.ac.uk (8.11.6+Sun/8.11.6) with ESMTP id gA3AEFo22312 for ; Sun, 3 Nov 2002 10:14:15 GMT Sender: chandra@ysbl.york.ac.uk Message-ID: <3DC4F62D.542A528F@ysbl.york.ac.uk> Date: Sun, 03 Nov 2002 10:10:54 +0000 From: Chandra Verma X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: MPI Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks very much to rick venable, the solution to using two dual processor machines for running a program with MPI libraries is: if the machines are called rand100 and rand101 then rand100 0 charmm rand100 1 charmm rand101 1 charmm rand101 1 charmm chandra