Dear all,<br><br>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:<br><br>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.<br>
<br>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.<br><br>This is the pull section in the mdp file:<br>
<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = N N Y <br>pull_start = yes ; define initial COM distance > 0<br>pull_ngroups = 1<br>pull_group0 = Protein<br>pull_group1 = Metal<br>
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns<br>pull_k1 = 3000 ; kJ mol^-1 nm^-2<br><br>Thanks in advance for your help<br><br>Jon Mujika<br>