Dear List
I have done a MD simulation for my ligand-receptor complex for 1ns. I analyzed the trajectory file and calculated the RMSD only for ligand during the simulation. The RMSD was constant during MD until in a distinct period of time it was fluctuated significantly and then reached to its constant value. I would like to know the binding energy for each frame. I tried to calculate the binding energy for each frame during MD but I have problem with it. I manged to extract the snapshots (using mm-pbsa perl version) but when I was trying to obtain binding energy for complex, it did not work. The error was referred to the following site:
http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
I changed the fillratio to 4 but it did not work.
Any help in this regard would be highly appreciated.
CheersMaryam
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Received on Wed Jun 17 2015 - 04:30:02 PDT
