From chemistry-request@server.ccl.net Sun Aug 26 02:37:20 2001 Received: from chem.ufl.edu ([128.227.16.141]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7Q6bKM00960 for ; Sun, 26 Aug 2001 02:37:20 -0400 Received: from chem.ufl.edu (chem.ufl.edu [128.227.16.141]) by chem.ufl.edu (8.9.1/8.9.1/map) with ESMTP id CAA21264 for ; Sun, 26 Aug 2001 02:37:20 -0400 (EDT) Date: Sun, 26 Aug 2001 02:37:19 -0400 (EDT) From: "Xiang(Simon) Wang" To: CHEMISTRY@ccl.net Subject: Re: CCL:Warning Message in Charmm: STRING TOO SMALL (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: Last October I asked the question about the warning message from the CHARMM. Sorry that I forgot to summarize the answers at that time. Recently I received several messages inquiring the answers. So I forward Rick Venable's answer here. Thanks for his answer. Regards, Simon WANG ---------- Forwarded message ---------- Date: Mon, 2 Oct 2000 19:54:58 -0400 From: Rick Venable To: "Xiang(Simon) Wang" Subject: Re: CCL:Warning Message in Charmm: STRING TOO SMALL On Mon, 2 Oct 2000, Xiang(Simon) Wang wrote: > I met the following warning message when reading thousands of TIP3 > molecules in Charmm: > > ***** LEVEL -1 WARNING FROM ***** > ***** STRING TOO SMALL > > Please help me if you know how to avoid such warning. Thanks. Because a 4-char string is used for the RESID (residue ID number) in CHARMM, you can only have 9999 water molecules within a single segment. There's an easy fix-- just split your waters into more than one segment, each with less than 10,000 molecules. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Sun Aug 26 03:40:47 2001 Received: from eyou.com ([61.136.62.73]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7Q7eGM03089 for ; Sun, 26 Aug 2001 03:40:46 -0400 Received: (qmail 83012 invoked from network); 26 Aug 2001 15:40:05 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.1 with SMTP; 26 Aug 2001 15:40:05 +0800 Received: (qmail 46555 invoked by uid 65534); 26 Aug 2001 15:40:06 +0800 Date: 26 Aug 2001 15:40:06 +0800 Message-ID: <20010826154006.46554.qmail@eyou.com> From: "王明韬" To: CHEMISTRY@server.ccl.net Reply-To: "王明韬" Subject: help! Dear all: Now, I want to study the interaction of some ligands with metalloprotein containing metal. However, I donnot know how to get the AMBER force field parameters for metal cobalt. Can you kindly give me suggestion? sincerely, Wang Mingtao 08,26,01 --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽 From chemistry-request@server.ccl.net Sun Aug 26 02:40:57 2001 Received: from epimetheus.hosting4u.net ([209.15.2.70]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7Q6evM01096 for ; Sun, 26 Aug 2001 02:40:57 -0400 Received: (qmail 15894 invoked from network); 26 Aug 2001 06:40:57 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 26 Aug 2001 06:40:57 -0000 Received: from yersina ([202.138.18.39]) by proinformatix.com ; Sun, 26 Aug 2001 01:40:52 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: AUTODOCK Date: Sun, 26 Aug 2001 16:39:31 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Hi everyone, I am trying to get a clear idea on how to define a volume in space where the ligand is restricted before starting the docking simulation. Which parameters control these features? Cheers Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Sun Aug 26 14:28:15 2001 Received: from elin.scali.no (IDENT:root@[62.70.89.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7QISEM03125 for ; Sun, 26 Aug 2001 14:28:14 -0400 Received: from localhost (ole@localhost) by elin.scali.no (8.11.0/8.11.0) with ESMTP id f7QISDK24943; Sun, 26 Aug 2001 20:28:13 +0200 Date: Sun, 26 Aug 2001 20:28:13 +0200 (CEST) From: "Ole W. Saastad" To: cc: Subject: G98/linda compilation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am trying to put together g98 and Linda. We have evaluation copies of both softwares, but not the two as a unit. I want to test the performance of our new ScaIP for this combination. Many Scali clusters could take advantage of its SCI interconnect through ScaIP. ScaIP runs very well with Linda alone, we get latency slightly less than the one for ethernet and a bandwidth more than three times that of ethernet. It might be that Linda/g98 might benefit from this higher bandwidth and somewhat lower latency. I have no information about the average package size for g98/Linda. How do you compile g98 for linda? I have more or less managed to compile g98 by changing the lines in bldg98 where you specify exe or linda. if ($dolink) then $makename -f $locmake $makeflag exe $makename -f $locmake $makeflag linda endif I had some problems with fork and wait. At present I run with two empty routines for wait and fork. This is not correct and a solution is needed. After I have compiled I have files called both .exe and exel, the latter beeing the Linda executables. How do I run g98 with these Linda executables ? Just running it a usual ( ./g98 ) does not start Linda, it does however run scalar the normal way. Some help on how to run Gaussian in combination with Linda would be very helpful. Best regards Ole W. Saastad Scali A/S.