CPPTRAJ Remove water

Original Example

CPPTRAJ can be used to remove explicit water from the simulation. To do this, make 2 files: 1) Strip water from trajectory, and 2) save new topology file.

1. Strip water from trajectory (traj1.in)

   • Load topology/trajectory files

   • autoimage re-orients the solute in the water box

   • strip removes the residues WAT and counterions

   • Fit new trajectory to alpha carbons

   • Save as dry-prod.nc

parm step3_pbcsetup.parm7
trajin prod.nc
autoimage
strip :WAT,Na,Cl
rms @CA
trajout dry-prod.nc 
go

2. Make a new topology file (traj2.in)

parm step3_pbcsetup.parmm7
parmstrip :WAT,Na,Cl 
parmwrite out dry-step3.parm7 
go

Run these commands with CPPTRAJ

cpptraj traj1.in
cpptraj traj2.in