# tleap commands file to build a monosaccharide
# with a Sulfate group instead of the Acetyl group
# at the N atom in position 2.
#
source leaprc.GLYCAM_06
# Uncomment the following line if you want to use
# the sulfate charges from GLYCAM website:
#
#loadamberprep sulfate.prep
#
# Uncomment the following line if you want to use
# the sulfate charges from ALTONA article:
#
loadamberprep sulfate_Altona.prep
#
set default PBradii mbondi2
glycan = sequence { ROH 0YA }
#
remove glycan.2 glycan.2.C2N 
remove glycan.2 glycan.2.O2N 
remove glycan.2 glycan.2.CME 
remove glycan.2 glycan.2.H1M 
remove glycan.2 glycan.2.H2M 
remove glycan.2 glycan.2.H3M 
set glycan tail glycan.2.N2
#
glycan = sequence { glycan SUL }
#
# Uncomment the following 2 lines if you want to use
# the N and H atoms charges (together woth sulfate
# charges) from ALTONA article:
#
set glycan.2.N2  charge -0.8900
set glycan.2.H2N charge  0.3210
#
charge glycan
savepdb glycan linear_glycan.pdb
saveamberparm glycan linear_glycan.parm7 linear_glycan.crd
quit