Dear Amber Users,
Greetings.
I would like to calculate B-factor for only ~10-15 water molecules (closest to the ligand).
Hbond analysis shows that there are 4-5 water molecules making strong (high occupancy and lifetime) H-bond interactions with the
binding site residues as well as the ligand. I am not sure how to accomplish this task.
I am familiar with calculating bfactors for residues (after rms fitting with the reference (average) structure).
what I have tried sofar ?
I created a new trajectory with Na+ stripped and only with closest 50 waters (the water molecules visually show huge fluctuations).
I am not really sure that the closest water molecules that are kept as closest remain the same through out the trajectory.
Now I am doing the bfactor calculation with the new trajectory.
step 1: average structure
step 2: rms fit with average
step 3: bfactor
Am I on the right track ? Please suggest me if I am doing anything wrong ?
Thanks,
Senthil
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Received on Wed Jul 25 2012 - 09:30:06 PDT
