View source for Remove waters from trajectories

use ptraj to delete the waters from the coordinate file.  
Make an input script for ptraj:
  trajin 10md.trj.gz 1 1000 1
  reference system.leap.crd
  rms reference out rms_out ::1-274@CA
  solvent byres :WAT
  closestwater 1 :81 first
  trajout new10md.dcd charmm nobox

run ptraj.

use rdparm to remove the waters from the parmtop file:

write rdparm in command line.

Type old parm file name (the one you gave to ptraj) when prompted.

Type stripwater

type the numbers of waters you wish to keep and new parm file name when prompted.

THIS MAKES AN AMBER7 PARM FILE

NOTE: if you wish to have a parm file with no waters use tleap to produce this file.

This command is if you wish to have fewer waters.

An alternative way to make a parm file is to specify a number of waters in your pdb file and run it though tLEaP.  
by default tLEaP uses the TIP3P parameters.