AMBER Archive (2004)

Subject: Re: AMBER: ptraj-closestwaters command

From: Thomas E. Cheatham, III (
Date: Mon Jul 12 2004 - 15:38:41 CDT

> Just wondering if someone can clarify what this sentence means in the ptraj
> documentation for closestwaters:
> "If "oxygen" or "first" are specified, only the distance to the first atom
> in the solvent molecule (to each atom in the mask) is measured. "
> Also is it possible to select waters that are closest to atoms rather than
> just residues?

The closest water command basically looks for the shortest distances
between your solvent (water) and the atoms specified. It is an expensive
command since it has to calculate all the distances.

The command is fairly general. You can select the closestwaters to any
particular set of atoms or residues. You can also redefine what is
solvent to find, for example, the closest ions. [One limitation of the
command is that the water looses it's "name" i.e. if you select 10 waters,
the waters get renumbered 1-10 loose their previous identity. This means
you cannot do diffusion or other calculations that require precise
correspondence of a water from frame to frame.]

So, to find the closest 25 waters to a bound drug in an active site, say
residue DRG,

  trajin mdcrd
  trajout mdcrd_closest_25
  closest 25 :DRG

If my trajectory has already been imaged, I can speed up the calculation
significantly by not imaging. I can further speed it up by using the
distance to the water oxygen rather than the oxygen + 2 hydrogens.

  trajin mdcrd
  trajout mdcrd_closest_25
  closest 25 :DRG oxygen noimage

Now let's say I want to find the closest 10 sodium ions (Na+) to the
carboxy oxygens of all the asparates:

  trajin mdcrd
  trajout mdcrd_Na+_10
  solvent byres :Na+
  closest 10 :ASP_at_OD?

I hope this helps; e-mail if you need further clarification. Also, in
general with ptraj, it is sometimes helpful to read the comments in the
source code (in actions.c, transformX where X is the name of the command)
to get an idea of what the program is (or is not) doing.

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