loop-to-helix change during SMD

From: yp sun (sunyeping_at_yahoo.com.cn)
Date: Mon Dec 31 2012 - 05:17:53 CST

Dear NAMD user,
I now want to simulate the low pH induced-conformational change in a protein. The protein has two chains and it is predicted than when pH drops, chain A disrupts and chain B undergo major conformational change, including a loop-to-helix change. Besides, some residues in chain A may infleunce this procedure. Could you tell me if SMD can simulate this procedure: can I using  SMD to pull chain A away so that the predicted conformational changes in chain B will be visualized. Is there any script that need to be add to the conf file to ensure the conformational change in chain B occur?  Or will these confornational change spontaniously happen when chain A is pull away just as in the real world? Thanks.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

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