Re: extracting waters from DCD

From: Joshua A. Speidel (
Date: Wed Aug 09 2006 - 09:42:34 CDT

Hello Nar,

Writing a DCD file with a specific number of waters closest to the
solute is possible with the MMC program by Mihaly Mezei (link at
bottom). The FILT command will take care of that task for you.

When I've done this, first I used the VMD1.8.4 Tcl interface to
determine approximately the number of waters with the cutoff I am
interested in:
[atomselect $mol "water and within 3.5 of protein"] num
For completeness, you could run this command on many frames of the
trajectory, and take the average number of waters. The average number of
waters within the cutoff (rounded to the nearest integer) is the input
to the FILT keyword in MMC.

To load the resulting DCD into VMD, you would need a new PSF with the
correct number of water molecules.

As noted, the 'idenitity' of the water molecules would be lost.

There are many other tools in MMC that specifically analyze of water
including proximity analysis tools, generic water binding site
calculations, radial distribution functions, and more.

As a final caveat, if the number of waters within your cutoff varies
greatly, this is probably not a great solution. Using this technique
implies that the number of waters within your cutoff is rather
constant. If using the MMC program for your analysis, then the native
MMC binary format allows for variable numbers of atoms (from Grand
Canonical Ensemble simulations). This file format is not supported in
VMD, so visualization can be difficult. Again, using the FILT command
allows for selection of waters in the 1st, 2nd or 3rd hydration shell
and other options.

Best wishes,


Nicholas M Glykos wrote:
>> 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.
> Nicholas

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