AMBER is located in /usr/groupS

How to Protonate crystal structures:

protonate -d data-file-name -i input-pdb-file -o output-pdb-file

for example:

/usr/groupS/Amber6/amber6/exe/protonate -d /usr/groupS/Amber6/amber6/dat/PROTON_INFO.Brook -i /chem/lawrence/RNA_PDB/ur0015.pdb -o /chem/lawrence/RNA_PDB/ur0015-H.pdb