Ming & Wall (2005) Quantifying Allosteric effects in Proteins. PROTEINS: Structure, function and bioinformatics
http://www3.interscience.wiley.com/cgi-bin/fulltext/110445470/HTMLSTART They perform normal mode analysis for enzyme/apo-enzyme. Gives brief of preparation for analysis. Josiah Zayner _____ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Anirban Ghosh Sent: Friday, June 29, 2007 1:06 AM To: [email protected] Subject: [gmx-users] Energy Minimization Protocol for running Normal ModeAnalysis Hi, I am new to GROMACS. I want to perform Normal Mode Analysis of a protein. For that I require a well minimized structure. I have minimized my structure using steepest descent and conjugate gradient. But the structure seems to have got struct in a local energy minima. How should I proceed to get a well minimized structure in order to go for Normal mode Analysis? Please suggest any protocol. Regards, -- Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Hyderabad - 500 046 Andhra Pradesh India
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