Re: extracting waters from DCD

From: Neelanjana Sengupta (
Date: Tue Aug 08 2006 - 15:57:56 CDT

If your system contains only protein and water (ie. no counterions, etc),
this selection should work: "all and not (resname TIP3 within 3.5 of
(protein and not hydrogen))".
It appears cumbersome, but you'll be able to parse it.

On 8/8/06, Narender Singh Maan <> wrote:
> Dear All,
> I have a trajectory file for my simulation of a protein in a big water
> box. Now to reduce the size i can extract and writeout the trajectory for
> 'just the protein' from this system by using "catdcd" but my aim is to
> extract some waters also (only those water molecules which are within 3.5Ang. of the protein surface...for each frame).Any suggestions would be of
> great help.
> thanks
> Nar

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