#
# Create a bond between the oxygen of Ser195 and the carbon of the Trp252-Thr253 peptide bond
#
connect (atomno=2737) (atomno=3485) single
#
# Create a bond between the hydrogen of Ser195 and the imidazole nitrogen of His57
#
connect (atomno=2742) (atomno=760) single
#
# Delete all hydrogen bonds (they mess up the geometry optimization)
#
select
hBonds delete
#
# Delete the bond between the hydrogen and oxygen of Ser195
#
connect (atomno=2737) (atomno=2742) delete 
#
#  Optimize the geometry of Ser195
#
delay 2
minimize SELECT (195) STEPS 100 
select 195
#
#  Run the command "write PDB" in the JSmol console after the minimize has finished
#
#  The coordinates of the selected atoms will appear in the console.
#  Copy them to the appropriate location.
#