Re: AMBER: Ptraj: watershell and distance

From: Thomas Cheatham III <>
Date: Thu, 1 Feb 2007 11:46:04 -0700 (Mountain Standard Time)

> When I use "watershell" command in the Ptraj to calculate the number of
> the waters in a certain distance, I am just thinking, is it possible to
> calculate this number within a centain distrance from the center of mass
> of the molecule?

This is not supported directly, in part because I do not see the reason
why this would be necessary. The intent of the command is to measure the
waters that are closest to the solute, and this normally means those that
are on the surface. If we have an oblong molecule, the closest waters
would be something like:

    w w w w w w
  w ----------- w
    w w w w w w

rather than the closest to the center of mass which would be:

       w w w
      w w w w
      w w w w
       w w w

If you know what atom is closest to the center of mass, you could do the
closest to this atom and be close to what you want...

> I have the same problem when I use "distance" command to calculate the
> distance between the specified atoms to the center of mass of the

This should not be a problem with the distance (or angle) commands as
these automagically use the center of mass of the atom selection. So, if
you wanted to measure the distance of the center of mass of a water
(residue #999) to the center of mass of your protein (let's assume it has
100 residues), you would do

  distance d1 out d1.dat :999 :1-100

I hope that clarifies things.

-- tec3 . utah . edu

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Received on Sun Feb 04 2007 - 06:07:35 PST
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