# ----- 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" } { "Ng" "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" } } # # load the main paramter set # glycam_06 = loadamberparams GLYCAM_06h-1.dat ## # # load all prep files for polysaccharides # loadamberprep GLYCAM_06h.prep # # load lib files # # for attaching glycans to proteins loadOff GLYCAM_amino_06h.lib loadOff GLYCAM_aminoct_06h.lib loadOff GLYCAM_aminont_06h.lib ## add residue maps for linking glycans to proteins ## Note! use of these requires sourcing the ff12SB leaprc and loading the amino ## libraries commented out 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" } } # # for explicit solvent and ions # # the following assumes most users want to use tip3p as the # explicit solvent model # this can easily switched by the following commands in leap: # WAT = TP5 # loadamberparams frcmod.tip5p # loadOff solvents.lib # solvents HOH = TP3 # set water model WAT = TP3 loadOff ions08.lib # load ions library # to use ions for TIP5P, you will need to use a different frcmod below ionsff = loadamberparams frcmod.ionsjc_tip3p # set ion params for TIP3P