Moving on towards another level ....
Recently, I tackled a simple approach of choosing closest waters for mmpbsa. Now, I aim to put ONLY buried water molecules into mmpbsa calculations. I am aware that in MD it is not the same water molecule in every frame. Is my goal possible to achieve ?
To my knowledge, the program NACCESS can identify buried water and it requires PDB as input. On the other hand, MMPBSA requires a trajectory as input. Clearly, I have to set-up a strategy to satisfy each programs.
I thought of strategy by "unbuilding" followed by "rebuilding" of trajectory.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step-1: Unbuilding trajectory
1a. Take snapshots from input trajectory and convert to its corresponding pdb file
1b. Using the pdb output from 1a, use naccess program to identify buried water
1c. Remove the non-buried water
Step-2: Rebuilding trajectory
Combine all trajectories. Make a corresponding topology and feed into mmpbsa for binding energy calculations.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Input trajectory for step-1a contains bulk TIP3P waters. To do preliminary filtering for input in step-1a, two ptraj options are available:
OPTION-1 Use closest command to select 10 water molecules at nearest distance to ligand. Output expected is solute (protein+ligand) and solvent (10 water). This output will be used as input trajectory for step-1a.
OPTION-2 Use strip command to strip all atoms further than 3 angstroms of ligand. Output of number of selected water will vary in each frame, and this could cause problem when this input goes through rebuilding stage of trajectory.
Bottomline, it is easy to unbuild the trajectory but the challenge lies on rebuilding it.
I hope to receive feedback from the forum.Thanks.
Amor
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Received on Wed Aug 25 2010 - 04:00:03 PDT
