Dear Sir,
I apply MD simulation to investigate protein-ligand complex. I use cpptraj script to analysis hydrogen bond surly. The version of cpptraj which I use is ambertools14. The script see the appendix. I would appreciate your help in correct formation of the cpptraj command. I can get the information about hydrogen bond that formed by residue and residue, residue and ligand, residue and solvent water. But what I want is the hydrogen bond between residue and water molecule, the water is included in the complex rather than solvent water. In my system, the water in the complex and the solvent water are both named "WAT". Looking forward to your reply. THANK YOU VERY MUCH!
Sincerely,
Liyan
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Received on Thu Jun 30 2016 - 18:30:02 PDT
