#!bin/bash

# prepare parameter and topology file and coordinate file for glycosylated 1dr9
source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.GLYCAM_06j-1
g1dr9 = loadPdb "1dr9_tleap.pdb"
bond g1dr9.16.SG g1dr9.82.SG
bond g1dr9.128.SG g1dr9.182.SG
solvateOct g1dr9 TIP3PBOX 14.0 
#addIons g1dr9 Na+ 20 Cl- 24
savepdb g1dr9 g1dr9_tleap.pdb
saveAmberParm g1dr9 solvated_g1dr9.top solvated_g1dr9.crd
quit 
