I have read several posts regarding water calculations in several ways for different purposes done. But it seems to me that the goal I want to achieve needs relevant feedback from the forum.
I have a system (protein + peptide + ligand) with 200 residues in total and note that ligand has a phosphate group. I want to identify the water molecules (TIP3P models) found at the interface between the ligand and protein. I need to identify which water molecules are at the interface so I can use it as input for binding energy calculation by MMPBSA. Here are the steps formulated for water identification:
1) Calculate the water within 3.5Angstroms using the trajectory input. The expected outcome is (P+L+Wi) such that P=protein, L=ligand, and Wi=water at ith frame. From the output, remove all hydrogen molecules in water.
2)Calculate accessibility by filtering out WAT.O (Water oxygen) within >0.50Angstroms
3) Repeat step 2 to get only the buried water molecules remaining at interface.
One suggestion I got is to make a script to do in one shot the above three steps. I think about it but am not sure if one straightforward script can do the task.
I approached the problem by trying to do it one-step-at-a-time. For step 1 above, I implemented ptraj. Using ptraj h-bond distance 3.5 analysis, it gave me an output of P+L+Wi, however looking at Wi seems to be so enormous from the list as expected.
For step2, I need the trajectory that contains P+L+Wi with stripped hydrogens generated from step1. I have not proceeded to step2 yet.
To get the trajectory P+L+Wi, it seems the way out is to use the ptraj-hbond output to select interacting atoms, but as noted Wi in the list is quite long to do manual selection one-by-one.
I also thought of using LIGPLOT program to identify buried water molecules but my input is a trajectory not a pdb. I know I can generate pdb from snapshots in trajectory but how would you take it for several thousands of snapshots pdb? Bottomline, I only need to identify the water at interface based on the trajectory.
Amor
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Received on Sun Aug 15 2010 - 21:00:03 PDT
