[gtkleap]$ source leaprc.GLYCAM_06	
#verbosity 1
# ----- leaprc for loading the Glycam_06 carbohydrate force field
# also contains atom types for lipids
#
#       load atom type hybridizations
#       (includes atom types relevant to lipids)
#
#
addAtomTypes{ 
        { "C"   "C" "sp2" }
        { "CG"  "C" "sp3" }
        { "CY"  "C" "sp3" }
        { "CK"  "C" "sp2" }
        { "CT"  "C" "sp3" }
        { "CJ"  "C" "sp2" }
        { "CP"  "C" "sp3" }
        { "H"   "H" "sp3" }
        { "H1"  "H" "sp3" }
        { "H2"  "H" "sp3" }
        { "HA"  "H" "sp3" }
        { "HP"  "H" "sp3" }
        { "HC"  "H" "sp3" }
        { "HO"  "H" "sp3" }
        { "HW"  "H" "sp3" }
        { "N"   "N" "sp2" }
        { "NT"  "N" "sp3" }
        { "N3"  "N" "sp3" }
        { "OH"  "O" "sp3" }
        { "OS"  "O" "sp3" }
        { "O"   "O" "sp2" }
        { "O2"  "O" "sp2" }
        { "OW"  "O" "sp3" }
        { "OY"  "O" "sp3" }
        { "S"   "S" "sp3" }
        { "SM"  "S" "sp3" }
        { "P"   "P" "sp3" }
}
## add residue maps for linking glycans to proteins
## Note! use of these requires sourcing the ff99 leaprc and loading the amino
##      libraries in the load libs section
addPdbResMap {
        { 0 "OLS" "NOLS" } { 1 "OLS" "COLS" }
        { 0 "OLT" "NOLT" } { 1 "OLT" "COLT" }
        { 0 "OLP" "NOLP" } { 1 "OLP" "COLP" }
        { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
        { 0 "NLN" "NNLN" } { 1 "NLN" "CNLN" }
}
#
#       load the main paramter set
#
glycam_06 = loadamberparams GLYCAM_06c.dat
Info: ignoring unknown atom type: NH
Info: while reading DIHE. Input: NH CG CG SM   1    0.45          0.0             3.         ****Sameer
Info: ignoring unknown atom type: NA
Info: ignoring unknown atom type: N2
Info: ignoring unknown atom type: N*
Info: ignoring unknown atom type: NC
Info: ignoring unknown atom type: NB
Info: ignoring unknown atom type: NP
Info: ignoring unknown atom type: NO
Info: ignoring unknown atom type: C*
Info: ignoring unknown atom type: CA
Info: ignoring unknown atom type: CB
Info: ignoring unknown atom type: CC
Info: ignoring unknown atom type: CN
Info: ignoring unknown atom type: CM
Info: ignoring unknown atom type: CQ
Info: ignoring unknown atom type: CW
Info: ignoring unknown atom type: CV
Info: ignoring unknown atom type: CR
Info: ignoring unknown atom type: CA
Info: ignoring unknown atom type: CX
Info: ignoring unknown atom type: CD
##
#
#       load all prep files for polysaccharides
#
loadamberprep GLYCAM_06.prep
#
#       load lib files
#
# for attaching glycans to proteins
loadOff GLYCAM_amino_06.lib
loadOff GLYCAM_aminoct_06.lib
loadOff GLYCAM_aminont_06.lib
#
# for explicit solvent
loadOff solvents.lib
HOH = TP3
WAT = TP3
#       assumes most users want to use tip3p as the explicit solvent model
#       but this can easily switched by the following commands in leap:
#       WAT = TP5
#       loadamberparams frcmod.tip5p
[gtkleap]$ glycan = sequence { ROH 4YB 4YB 3MB 0MA } 
Sequence: ROH
Sequence: 4YB
    tail: 2 O1
    head: 3 C1
Sequence: 4YB
    tail: 29 O4
    head: 30 C1
Sequence: 3MB
    tail: 56 O4
    head: 57 C1
Sequence: 0MA
    tail: 77 O3
    head: 78 C1
[gtkleap]$ impose glycan {3 2} { {C1 O4 C4 H4 0.0} }
[gtkleap]$ impose glycan {4 3} { {C1 O4 C4 H4 0.0} }
[gtkleap]$ saveamberparm glycan glycan.top glycan.crd  
Error: sparm type does not exist!