Hi - I'm trying to simulate the folding of a protein (for purely aesthetic reasons) and was hoping to use AMBER to do this from an extended strand structure. The protein is around 160 amino acids. I actually took the crystal structure of the folded protein and generated around 20K NMR-type distance restraints. I was hoping to use targeted MD to do this using the crystal structure as the target structure. Does anyone have a sense of whether this will work or not? Initially, I'm attempting to minimize the extended strand starting structure as done in Ross Walker's tutorial, but it seems that the system may be too big. Any ideas would be greatly appreciated.
Thanks,
Brad
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Received on Thu Oct 28 2010 - 14:00:07 PDT
