AMBER Archive (2006)

Subject: Re: AMBER: watershell and image commands

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Thu Nov 30 2006 - 18:04:04 CST

Thanks a lot for your help. I got it. I do the test as you said, I found the coordinate of the molecule is the same, the coordinates for water are very little diffferent.

Thomas Cheatham <tec3_at_utah.edu> wrote:
> I am trying to use "watershell" to calculate the waters in the
> solvation shells. But one thing is confused me. When I use the "image"
> command to generate the waters to the primary box, I found 2 different
> results. One is the molecules in the center of the box, one is not. I am
> just wondering whether it will influence the "watershell" to calculate
> the waters. Here are the 2 ways to re-image the trajectory file:
>
> trajin md.mdcrd.gz
> trajout test2.mdcrd
> center origin :1-25
> image origin familiar
> go
>
> trajin md.mdcrd
> trajout test1.mdcrd
> center 1-25
> image familiar
> go
>
> Is there someone know that? Which one will be correct to choose to calculate the "watershell"?
> Thank you very much!

If you used these exact scripts, the second one did not center anything
since it would not recognize "1-25". You need ":1-25" as in the first
script. If the correct syntax was indeed used, then the first
centers/images at the origin and the second center/images at the box
center but both should give equivalent water shells, assuming that
residues 1-25 do not span the box...

What I would do is read in a single frame in each case and output a PDB
file and look at them to "see" how they look/differ.

  trajin md.mdcrd 1 1 1
  trajout snapshot pdb
  center :1-25
  image familiar
  go

--tom

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Esther B.

 
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