Jason, thanks a lot ! Your detailed explanation made me more understand what to take precautions in the designed methodology.
Statistical sampling is the next issue to tackle here. Without the water calculation in mmpbsa, I took 5000 snapshots as input. Now, adding water for calculation choosing particularly only buried waters, steps 1b & 1c below cant be done manually if 5000 frames are to be taken. I am not expert in writing scripts.
Suggestions please .....
Amor
--- On Wed, 25/8/10, Jason Swails <jason.swails.gmail.com> wrote:
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Water deeply buried for MMPBSA calculations
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Wednesday, 25 August, 2010, 7:19 PM
Hello,
On Wed, Aug 25, 2010 at 6:54 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> 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 ?
>
This sounds like the "closest" command that you've been asking about
before.� One thing you have to make sure of, though, is that you keep the
SAME number of water molecules in each frame.� MM/PBSA will not be able to
take into account a variable number of water molecules in each frame.
>
> 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
>
Ptraj can do this quite easily.
> 1b. Using the pdb output from 1a, use naccess program to identify buried
> water
> 1c. Remove the non-buried water
>
Again, ptraj can do this if naccess can't.
>
> Step-2: Rebuilding trajectory
>
> Combine all trajectories. Make a corresponding topology and feed into
> mmpbsa for binding energy calculations.
>
ptraj can do this as well.� Just trajin the PDB files.
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> 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.
>
This is your best option.
>
> 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.
>
If there are a different number of water molecules each frame, then a
*single* topology file will not work for every frame (since each frame could
have a different number of atoms/water molecules.� This case will not work
for MM/PBSA.� Moreover, it doesn't make sense to compare an energy with 10
water molecules to an energy with 20 water molecules.
Hope this helps,
Jason
>
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 26 2010 - 04:30:03 PDT
