Try the "closest" command in ptraj. If there's a specific number of water
molecules that you expect at the interface, you can always keep the closest
waters to a specific residue/atom using that command. That will probably
work better than h-bond analysis, since that will require a lot more memory
to complete.
Good luck!
Jason
On Sun, Aug 15, 2010 at 11:51 PM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 16 2010 - 06:30:05 PDT
