source leaprc.ff94

set default PBradii mbondi2

thio = loadpdb thioredoxin_chaina_modified.pdb

#Add the disulphide bond
bond thio.32.SG thio.35.SG

saveamberparm thio thio_ash.prmtop thio_ash.inpcrd

#Adjust the charges to match the Asp- charges from the paper
set thio.26.OD2 charge -0.8014
set thio.26.OD1 charge -0.8014
set thio.26.CG  charge  0.5307
set thio.26.HD2 charge  0.0000

saveamberparm thio thio_asp.prmtop thio_asp.inpcrd

quit