From: John Stone (
Date: Tue Feb 18 2014 - 13:17:04 CST

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  John Stone

On Tue, Feb 18, 2014 at 09:31:06AM -0600, KK R wrote:
> Hi,
> I have a result from NAMD simulation. I noticed that there were two water
> clusters around the ligand within the active site of the protein.
> Therefore, I tried to extract a set of protein+ligand+water (within 10A of
> ligand) from every frame of my DCD trajectory. I could accomplish it using
> the following script in the Tk console.
> --------------------------------------------------------------------------------------------------------------------------------
> set sel [atomselect top "{protein} or {resname LIG} or {water within 10 of
> (resname LIG)}"]
> set n [molinfo top get numframes]
> set outname "protligwater_"
> for { set i 0 } { $i < $n } { incr i } {
> $sel frame $i
> $sel update
> set name [format "%s%.9d.pdb" $outname $i]
> $sel writepdb $name
> }
> ---------------------------------------------------------------------------------------------------------------------------------
> where LIG is the segid for ligand
> But, the above script writes protein+ligand+(water residues as well as
> only part of water residues (like H or OH etc) lying within that radius
> around ligand).
> How to specify in the command line to select complete water residues lying
> within any particular radius, even if only part of some water resides with
> that radius?
> I hope that my question is clear to you all. If not, please let me know.
> Thanks again,
> Best regards,
> Roy

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