Re: extracting waters from DCD

From: Nicholas M Glykos (
Date: Wed Aug 09 2006 - 06:54:44 CDT

> 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 3.5 Ang. of
> the protein surface...for each frame).Any suggestions would be of great
> help.

Not easy: The number of water molecules around the solute (and within any
given cutoff, say 3.5A) will vary from frame to frame. What this implies
is that in the scenario you describe you can not have a constant-number-
of-atoms system.

I can imagine a solution where you decide to keep a constant number of
water molecules around the solute, and you don't care about the real
(PSF-wise) identity of individual molecules. As far as I know no such
program or script exists.


            Dr Nicholas M. Glykos, Department of Molecular 
        Biology and Genetics, Democritus University of Thrace,
    Dimitras 19, 68100 Alexandroupolis, GREECE, Fax ++302551030613
     Tel ++302551030620 (77620),

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