logFile leap.log
#
#
#               Making Branched Carbohydrates
#
# In general, the head atom is set to C1 in each sugar, where the tail atom
# varies depending on the sugar linkage.  For all sugars, the tail atom is
# specified as the glycosidic oxygen with the largest atomid, i.e. for the
# 2,3,4, linked sugars the tail atoms would be O4.  Therefore, it it possible
# to build the longest chain according to this convention and then connect
# the branched portions.  Simply changing the tail atom enables a different
# connection point for the unit, which can then be utilized to sequence to
# any branched residue/s.
#
#
# Example: Man9
#
# Mana1 - 2Mana1 \
#                  3
#                   Mana1
#                  6      \
# Mana1 - 2Mana1 /          6
#                            ManB-OMe
#                           3
# Mana1 - 2Mana1 - 2Mana1 /
#
#
# First, we must load the necessary parameters and prep files
#
source leaprc.glycam04
#
# Find the longest chain and use the sequence command to build it
# (See the manual for naming conventions)
#
part1 = sequence { OME VMB 2MA 2MA 1MA }
#
# Now set the tail atom of part1 to O3 of VMB
#
set part1 tail part1.2.9
#
# Join the first branch to the long chain
#
part2 = sequence { part1 VMA 2MA 1MA }
#
# Set the tail atom of part2 to O3 of VMA
#
set part2 tail part2.6.19
#
# Add the last branch
#
man9 = sequence { part2 2MA 1MA }
#
# The basic structure has been built, but it clearly does not have the optimal
# glycosidic torsion angles.
#
# Set the psi(1-6) torsion to 180 (C1-O6-C6-C5)
#
impose man9 { 2 3 4 } { { C5 C6 O6 C1 180.0 } }
#
# Set the omega angle of 6-linked sugars to 60.0 (O5-C5-C6-O6)
#
impose man9 { 2 3 }  {{ O6 C6 C5 O5 60.0 } }
#
# Set the phi angle of all a-linked (not 1-6 linked) sugars to -60.0
#
impose man9 { 4 5 6 7 8 9 10 } { { H1 C1 O2 C2 -60.0 } }
impose man9 { 6 2 } { { H1 C1 O3 C3 -60.0 } }
impose man9 { 9 3 } { { H1 C1 O3 C3 -60.0 } }
#
# Set the psi angle of all sugars to 0.0
#
impose man9 { 4 5 6 7 8 9 10 } { { C1 O2 C2 H2 0.0 } }
impose man9 { 6 2 } { { C1 O3 C3 H3 0.0 } }
impose man9 { 9 3 } { { C1 O3 C3 H3 0.0 } }
#
# Now we have a reasonable starting structure for AMBER min/md, but we need
# to save a topology and coordinate file as well as a pdb for later use.
#
saveamberparm man9 man9.top man9.crd
savepdb man9 man9.pdb
#
# Exit the program
#
quit
#
# For more info visit the GLYCAM website www.glycam.ccrc.uga.edu