AMBER Archive (2004)

Subject: Re: AMBER: H-bonded waters selection

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Nov 04 2004 - 23:05:24 CST

> I have a trajectory of solvated DNA and I want to analyse the hydration
> of my DNA. For this I'd like to re-save this trajectory with the DNA
> plus the water molecules that are H-bonded to it (that is get rid of
> waters not H-bonded to DNA and visualize with VMD). I tried to play
> around with ptraj and the trajout command but could not acheive that.

There are two general ways to do this with ptraj.

(1) closest

You can save the closest "N" waters to the DNA; this will create a new
trajectory of the DNA plus N waters. To view it with VMD, you would have
to either create a prmtop with that many waters or a PDB with that many
waters to load up prior to loading the trajectory. Note that water
residue numbers are not retained, i.e. waters are ordered now 1->N rather
than by their original numbers so it is not possible to "track" individual
waters with the post-processed trajectory (i.e. use commands like
diffusion).

closest 100 :1-10

will save the closest 100 waters around residues 1-10. Note that DNA
normally has a minimal hydration of something like 20 waters per base
pair (if I am remembering correctly).

(2) grid

It is possible to grid "atomic density" (used loosely here, realistically
what is binned is a count of selected atoms per grid element) around the
DNA and view this with chimera (available from the Computer Graphics Lab
at UCSF loading up an Xplor density file). This a really nice way to see
where tight waters, etc. are located.

a. center/image the water around the area of interest
b. rms fit to a common reference frame
c. grid the water (or ion) density

In a second run, do steps (a) and (b) and output a reference PDB (i.e. the
first frame) which average structures can be fit to and therefore
correspond to the grid.

Here is a portion of a ptraj input file that I use to construct a grid
around a portion of a double stranded DNA. My duplex has 22 base pairs.

  trajin traj.37.gz
  trajin traj.38.gz
  trajin traj.39.gz
  trajin traj.40.gz

  center :1-22 mass origin
  image origin center familiar
  center :1-44 mass origin
  image origin center familiar
  rms first mass out rms :1-44
  rms first mass out rms.middle :10-13,:32-35
  grid wat.grid 100 0.5 100 0.5 120 0.5 :WAT_at_O
  grid na.grid 100 0.5 100 0.5 120 0.5 @Na+
  grid cl.grid 100 0.5 100 0.5 120 0.5 @Cl-

  strip :45-99999

  average avg_0-5ns.pdb :1-44 pdb start 0 stop 5000
  average avg_5-10ns.pdb :1-44 pdb start 5000 stop 10000
  average avg_10-15ns.pdb :1-44 pdb start 10000 stop 15000

Note that dynamics of the molecule will smooth the grid (i.e. lower the
effective density). It takes a while to get a feeling for what the grid
represents.

I hope this helps.

p.s. you can also look at radial distribution functions, the hbond
routines to look at lifetimes of bound water, ...

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