Dear All, I planned to use the method introduced in the Umbrella Sampling on-line tutorial of Justin Lemkul (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).
But if a peptide is surrounded by a protein, which means the opening of the protein-complex is not large enough to allow the peptide to leave the protein without significantly breaking the conformation of the protein in the protein-peptide complex, is the Umbrella Sampling method still valid for the binding energy calculation? Will you please also show me in which part of the tutorial the direction of pull-apart is defined? We should process it in a direction the peptide can leave the protein, not the direction protein will bind the peptide much strongly. I am looking forward to getting a reply from you. Cheers, Acoot
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