From: Almira Ovagimyan (
Date: Thu Apr 11 2019 - 15:20:42 CDT


I wanted to find waters near a protein by the analysis script. However, when I try to load this script file to the VMD tkconsole by writing source findwater.tcl, I get this lines: usage: atomselect <command> [args...]Creating an Atom Selection: <molId> <selection text> [frame <n>] -- creates an atom selection function list -- list existing atom selection functions (type an atomselection function to see a list of commands for it)Getting Info about Keywords: keywords -- keywords for selection's get/set commands symboltable -- list keyword function and return typesAtom Selection Text Macros: macro <name> <definition> -- define a new text macro delmacro <name> -- delete a text macro definition macro [<name>] -- list all (or named) text macros

I used this script:

set sel [atomselect top "water and within 2 of protein"]
set n [molinfo top get numframes]
for { set i 0 } { $i < $n } { incr i } {
  $sel frame $i
  $sel update
  $sel writepdb water_$i.pdb
I want to display the number of water molecules near the protein. How can I see the result?