#!bin/bash

# prepare parameter and topology file and coordinate file for glycosylated 1I8L chain A
source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.GLYCAM_06j-1
g1I8LA = loadPdb "1I8LA_naming.pdb"
bond g1I8LA.16.SG g1I8LA.82.SG
bond g1I8LA.128.SG g1I8LA.182.SG
bond g1I8LA.19.ND2 g1I8LA.209.C1
bond g1I8LA.55.ND2 g1I8LA.210.C1
bond g1I8LA.64.ND2 g1I8LA.211.C1
bond g1I8LA.152.ND2 g1I8LA.212.C1
bond g1I8LA.173.ND2 g1I8LA.213.C1
bond g1I8LA.177.ND2 g1I8LA.214.C1
bond g1I8LA.192.ND2 g1I8LA.215.C1
bond g1I8LA.198.ND2 g1I8LA.216.C1
solvateBox g1I8LA TIP3PBOX 14.0 
addIons g1I8LA Na+ 55 Cl- 47
savepdb g1I8LA g1I8LA_leap.pdb
saveAmberParm g1I8LA solvated_g1I8LA.top solvated_g1I8LA.crd
quit 
