Dear Gmx Users, Dear Justin, I run pulling of my ligand away from my protein. Then I used Justin perl script to extract distances for umbrella sampling windows between my ligand and crucial residue of my protein (Isoleucine). The number of hydrogen bonds between ligand and protein during the pulling is app. 3 at the begining, then 4 in some frames and then obviously zero (when ligand dissociated). Would you use the 1st frame as a starting window when number of hbonds is 3 or further window when this is number is 4? Is spacing of 0.2 nm (pulling of app 6 nm) sufficent for the system where interactions are via hydrogen bonds and hydrophobic interactions only?
Thank you. Steven
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