From: jonas condes (jonamdtf_at_yahoo.com.mx)
Date: Fri Aug 18 2006 - 14:40:46 CDT
Hi, all. Well, I`m performing an SMD of the protein TFIIB. What I did at first is a search for a hinge region by using the program Dyndom. In this case my output are the values of the dihedral angles within the hinge region that are necessary in order to pass from one conformation to the other (open-closen or reverse). The protein consists of two cyclin subdomains and I want to see if I can pass from one conformation to the other. The problem now is that I don`t know how to input this information in any NAMD conf. file given that the only parameters I can state are the constant force: k and the constant velocity pulling: v, in order to direct my run in the direction of the dihedrals displacements! How can I do this?
* the outputs from my dyndom run are also attached in the message
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