# ----- 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 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" } } # # load the main paramter set # glycam_06 = loadamberparams /usr/local/programs/glycam06/parameters/Glycam_06_current.dat ## # # load all prep files for polysaccharides # loadamberprep /usr/local/programs/glycam06/prep_files/Glycam_06.prep # # load lib files # # for attaching glycans to proteins loadOff /usr/local/programs/glycam06/prep_files/indiv_amino_glycam_prep/Glycam_06_amino.lib loadOff /usr/local/programs/glycam06/prep_files/indiv_amino_glycam_prep/Glycam_06_aminoct.lib loadOff /usr/local/programs/glycam06/prep_files/indiv_amino_glycam_prep/Glycam_06_aminont.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