Article ID: 674 - Last Modified: May 16, 2011
Although I select Dock Rigidly from the Glide interface, the poses are distorted. What's causing the distortions in the conformations?
It is likely that the post-docking minimization (PDM) is responsible for the distortions. Some ligand strain can be introduced in fitting the ligand in the active site as Glide accommodates the rigid receptor structure. If you run the optional PDM step of Glide, close intra-ligand contacts can be relieved, but this can sometimes happen at the expense of transferring the high-energy clashes into distortions.
Try turning off the post-docking minimization (on the Output tab). You may end up with some close contacts in the ligand conformations, but the bond lengths and bond angles will stay at the input values.
Keywords: deformations, conformations, dock rigidly, change conformation, distortions
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