From chemistry-request@ccl.net Tue Jan 27 12:53:58 2004 Received: from servm.fc.uaem.mx (servm.fc.uaem.mx [148.218.36.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0RHrvSX011720 for ; Tue, 27 Jan 2004 12:53:57 -0500 Received: from rigel.fc.uaem.mx (rigel.fc.uaem.mx [148.218.36.120]) by servm.fc.uaem.mx (8.12.10/8.12.10) with ESMTP id i0RI1Dst011614 for ; Tue, 27 Jan 2004 12:01:13 -0600 Subject: CCL: Flyvbjerg and Petersen algorithm for macromolecules? From: Cesar Millan To: chemistry/at/ccl.net Content-Type: text/plain Message-Id: <1075204363.32228.6.camel/at/rigel.fc.uaem.mx> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.4-8mdk Date: Tue, 27 Jan 2004 11:52:44 +0000 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.6 required=7.0 tests=DATE_IN_PAST_06_12 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL readers! I have a question about the correlation between points on a molecular dynamics simulation. I want to know if the Flyvbjerg and Petersen algorithm (Error estimates on averages of correlated data, J Phys Chem, 91 (1), 1989.) can be used to molecular simulations of macromolecules. Does any one know any reference about these theme or an article with the use of these algorithm on macromolecules? I really appreciate your help. Cesar Millan Pacheco Facultad de Ciencias Universidad Autonoma del Estado de Morelos Cuernavaca, Morelos. From chemistry-request@ccl.net Tue Jan 27 10:16:54 2004 Received: from csiromail3.act.csiro.au (csiromail3.act.csiro.au [152.83.2.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0RFGqSX004777 for ; Tue, 27 Jan 2004 10:16:52 -0500 Received: from csiromail7.act.csiro.au (unknown [152.83.2.18]) by localhost.csiro.au (Postfix) with ESMTP id 3E62F139296 for ; Tue, 27 Jan 2004 15:18:43 +0000 (UTC) Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.act.csiro.au (Postfix) with SMTP id DD33A7352A for ; Wed, 28 Jan 2004 02:12:55 +1100 (EST) Received: from csiromail1.vic.csiro.au (csiromail1.vic.csiro.au [138.194.2.12]) by csiromail7.act.csiro.au (Postfix) with SMTP id 398BA7352A; Wed, 28 Jan 2004 02:12:51 +1100 (EST) Received: from [138.194.4.66] (vic066.dialup.csiro.au [138.194.4.66]) by csiromail1.vic.csiro.au (Postfix) with ESMTP id C3B7E138002; Wed, 28 Jan 2004 02:18:31 +1100 (EST) In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v612) Content-Type: multipart/alternative; boundary=Apple-Mail-4-272746132 Message-Id: <10369F14-50DC-11D8-A599-000A9579AE94_at_csiro.au> Cc: Kim Branson From: Kim Branson Subject: compiling DOCK on OSX Date: Wed, 28 Jan 2004 02:18:30 +1100 To: chemistry_at_ccl.net X-Mailer: Apple Mail (2.612) X-Spam-Status: No, hits=0.1 required=7.0 tests=HTML_MESSAGE,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Apple-Mail-4-272746132 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hi all, I'm looking at running DOCK on some G5 Xserves, so i'm trying to build UCSF DOCK 4.01 and DOCK 5 on osx (panther), has anyone done this? DOCK 4.01 and grid have a problem with: gcc -O2 -lm -c -o parm.o parm.c In file included from parm.c:10: /usr/include/sys/resource.h:81: error: field `ru_utime' has incomplete type /usr/include/sys/resource.h:82: error: field `ru_stime' has incomplete type /usr/include/sys/resource.h:119: error: parse error before "int32_t" /usr/include/sys/resource.h:124: error: parse error before "rlim_t" /usr/include/sys/resource.h:130: error: parse error before "fixpt_t" /usr/include/sys/resource.h:132: error: parse error before '}' token parm.c: In function `set_memory_limit': parm.c:356: error: storage size of `total' isn't known parm.c:356: error: storage size of `resident' isn't known make: *** [parm.o] Error 1 while with DOCK 5 the version of oelib is hard to build, since the configure script does not know about darwin. I'm trying a newer version of the oelib library from sourceforge (i'm not sure if one can mix and match the library versions? ). The version of mpich Version 1.2.2, August, 2001 also has trouble with the configure process. I'm hoping the new version of the library (1.2.5.2) might fix this, but if anyone has makefiles or tips for this version i'd appreciate it. cheers Kim --Apple-Mail-4-272746132 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Hi all, I'm looking at running DOCK on some G5 Xserves, so i'm trying to build UCSF DOCK 4.01 and DOCK 5 on osx (panther), has anyone done this? DOCK 4.01 and grid have a problem with: gcc -O2 -lm -c -o parm.o parm.c In file included from parm.c:10: /usr/include/sys/resource.h:81: error: field `ru_utime' has incomplete type /usr/include/sys/resource.h:82: error: field `ru_stime' has incomplete type /usr/include/sys/resource.h:119: error: parse error before "int32_t" /usr/include/sys/resource.h:124: error: parse error before "rlim_t" /usr/include/sys/resource.h:130: error: parse error before "fixpt_t" /usr/include/sys/resource.h:132: error: parse error before '}' token parm.c: In function `set_memory_limit': parm.c:356: error: storage size of `total' isn't known parm.c:356: error: storage size of `resident' isn't known make: *** [parm.o] Error 1 while with DOCK 5 the version of oelib is hard to build, since the configure script does not know about darwin. I'm trying a newer version of the oelib library from sourceforge (i'm not sure if one can mix and match the library versions? ). The version of mpich Version 1.2.2, August, 2001 also has trouble with the configure process. I'm hoping the new version of the library (Times1.2.5.2) might fix this, but if anyone has makefiles or tips for this version i'd appreciate it. cheers Kim --Apple-Mail-4-272746132-- From chemistry-request@ccl.net Tue Jan 27 12:02:42 2004 Received: from hotmail.com (bay13-f36.bay13.hotmail.com [64.4.31.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0RH2dSX009086 for ; Tue, 27 Jan 2004 12:02:39 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 27 Jan 2004 09:04:23 -0800 Received: from 202.141.142.9 by by13fd.bay13.hotmail.msn.com with HTTP; Tue, 27 Jan 2004 17:04:22 GMT X-Originating-IP: [202.141.142.9] X-Originating-Email: [vemaparna:at:hotmail.com] X-Sender: vemaparna:at:hotmail.com From: "Aparna Vema" To: chemistry:at:ccl.net Subject: Molecular dynamics run Date: Tue, 27 Jan 2004 22:34:22 +0530 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 27 Jan 2004 17:04:23.0045 (UTC) FILETIME=[9C83E350:01C3E4F7] X-Spam-Status: No, hits=1.3 required=7.0 tests=HTML_20_30,HTML_MESSAGE, MIME_HTML_NO_CHARSET,MIME_HTML_ONLY autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net

Dear CCL USers,

I have a huge protein Under study. I would like to subject it to MOlecular Dynamics. My forcefield limits me to take only 20 A of the protein from the active site. So i had to fix the protein 10A away from the active site and perform Molecular dynamics only for the active site. I continued MD with NVT ensemble.

Do the results i get are reliable. As i am fixing the protein to some extent do i need to compensate this constraint with some thing else.

Please let me know

Thanking you,

Aparna


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-Vema Aparna  Research Scholar
Prof. G.R. Desiraju's Group, School of Chemistry
University Of Hyderabad, Hyderabad - 500 046 INDIA

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