Dear all, I am trying to pull a metal out of the protein binding pocket following a cavity in the protein structure. I followed the tutorial, but I find few problems:
1) When the metal leaves the binding pocket, some ligands "follow" the metal, even that I restrained the position of protein atoms (force constant of 1000 or 3000). I would like to keep the protein as it is. 2) The metal does not leave the protein through the cavity. How can I define this? I can take a water molecule in the cavity as reference, but I do not how to deal with this. This is the pull section in the mdp file: pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = Metal pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 3000 ; kJ mol^-1 nm^-2 Thanks in advance for your help Jon Mujika
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