Restraint.vmd.script

#opens the file that has the atoms that are to be restrained
# if amber inputs do this
# mol load parm7 parm.file rst7 crd.file
# if namd inputs do this
mol load psf psf.file pdb pdb.file 

set case [atomselect top "all and noh or protein"]
# change atom selections to your protein
$case set beta 5 # this is the restraint this is high.
$all writepdb ./gdp.restraint01.pdb

quit