AMBER Archive (2009)
Subject: [AMBER] Simulation short peptide and protein interaction
From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Dear anyone who may concern this letter,
I want to carry out md on a small peptide (ligand, with 12 residues) and protein (receptor) system. I want to simulation the interaction whole process, namely, from the process of the ligand enter the pocket of the protein to it completely accommodated by the receptor. Do anyone have such experience? Can we use md to carry out this intention? How much time it needs? As far as I know, the association rate for this short peptide with its receptor is very slow. Now, I have docked the peptide to the door of the pocket.
Thanks for your help!