VMD-L Mailing List

From: KK R (kkres14_at_gmail.com)
Date: Tue Feb 18 2014 - 13:30:19 CST

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).
Can anybody suggest me about 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 in advance,

Best regards,
Roy