Hello,
On Mon, Aug 16, 2010 at 2:19 AM, Amor San Juan <amorsanjuan.yahoo.com>wrote:
> I want to write a follow-up in regard to my previous post below.
>
> Aside from ptraj hbond analysis, I also tried several ptraj commands
> including:
> a) grid = the aim of this command is to generate water density at hydration
> b)watershell= the aim of this command is to count the number of water
> molecules at 1st/2nd solvation shell
> c) closest= the aim of this command is to quantify the number of water
> molecules at 3.5A and 5A.
>
> In all those commands above, I am unable to identify the numbering of water
> buried at interface. Although the closest command can quantify the water
> molecules at specific distance, its numbering of water molecules were
> altered compared to the original numbering.
>
> My aim is to get the identity of the water molecules buried between the
> ligand-protein. Once the water identity is found, I will use this as input
> together with prot+lig for binding energy calculation in mmpbsa. What I mean
> to say in water identity is simply the water identity as reflected on its
> atom/residue number.
>
You don't need this really. Just create a new prmtop and trajectory file
with only the proper number of waters that you kept with the "closest"
command. Then it doesn't matter what the original numbering was in the
prmtop/trajectory file(s), it's simply the new numbers it has in the new
trajectory. Then feed this into MMPBSA and don't tell it to strip any
waters/ions. For example, if you're using MMPBSA.py, set strip_mdcrd=0 to
avoid stripping the trajectory file of any waters/ions. For mm_pbsa.pl,
just include the water atoms as part of the ligand or receptor atoms.
Hope this helps,
Jason
> amor
>
>
> --- On Mon, 16/8/10, Amor San Juan <amorsanjuan.yahoo.com> wrote:
>
> From: Amor San Juan <amorsanjuan.yahoo.com>
> Subject: How to identify water molecules at the interface ?
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Monday, 16 August, 2010, 11:51 AM
>
> 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 - 06:30:08 PDT
