#to translate whole system

atom trans vector="-$xce,-$yce,-$zce" select="ALL"

#to translate whole system to origin, i.e. reset geometric to origin

atom transto pos="0,0,0" select="ALL"

#to rotate whole system 180 degree along Z axis

atom rotate axisO="0,0,0" axisV="0,0,1" angle=180 select="ALL"

#to reorient the structure selected by matching the principal axis to

#Z,Y,X respectively 

atom reorient select="segn PROA" notrans=true

#to resort residue sequence for “seg SOLV”

atom resortseq istart=1 select="segn SOLV"

  #to rename residue name to “CYS” for “resn CYX CYM”

atom resn newname=”CYS” select="resn CYX CYM"

#to rename segment name to “PROA” for “seg A”

atom segn newname=”PROA” select="segn A"

#to rename atom name to “OH2” for all atom “name OW”

atom name newname=”OH2” select="name OW"

#to change residue sequence id to newiseq for all atom “name OW”

atom seq newseq=100 select="residue PROA 10"

#to change atom FF type to new type for all atoms selected

atom type newtype=¡±O¡± select="atom OH2"

#to set Langevin friction coefficient for all atom selected

atom lngfric value=5 select="name H*"

atom lngfric value=10 select="!name H*"

#to set charge to new value for all atom selected

atom charge value=0 select="resn CLA SOD"

#to make all Hydrogen to be heavy

atom mass value=12 select="name H*"

#to make the coordinates uninitiated for all atoms selected

atom resetcrd select="name H*"

buildunknowncoord   #rebuild coordinated according to FF

#to fix atoms selected

atom fix select="segn PROA"