From chemistry-request #at# 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
email: vemaparna:at:hotmail.com

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