logFile leap.log # # ----- leaprc for loading the GLYCAM-06EP carbohydrate force field # contains EPs to model lone pairs on oxygen atoms # with sp2 lone pairs of 0.45A and sp3 lone pairs 0.70A # no lone pairs on carboxyalate groups # ################# PLEASE NOTE ######################## ## ## Updated copies of the GLYCAM parameter and ## prep files can be downloaded from the GLYCAM ## web site's Documentation page: ## ## http://legacy.legacy.glycam.org/params ## ####################################################### # # load atom type hybridizations # addAtomTypes { { "H" "H" "sp3" } { "Ho" "H" "sp3" } { "H1" "H" "sp3" } { "H2" "H" "sp3" } { "HW" "H" "sp3" } { "Hc" "H" "sp3" } { "Oh" "O" "sp3" } { "Os" "O" "sp3" } { "O" "O" "sp2" } { "O2" "O" "sp2" } { "OW" "O" "sp3" } { "C" "C" "sp2" } { "Cg" "C" "sp3" } { "Ng" "N" "sp2" } { "EP" "" "sp3" } } # # load the main paramter set # glycam_06EP = loadamberparams GLYCAM_06EPb.dat # # load all prep files for polysaccharides including lone pairs # loadamberprep GLYCAM_06EPb.prep # # load water and ions # assumes most users want to use tip3p as the explicit solvent model # but this can be easily switched by the following commands in leap: # HoH = TP5 # WAT = TP5 # loadamberparams frcmod.tip5p # HOH = TP5 WAT = TP5 loadOff solvents.lib tip5pff = loadamberparams frcmod.tip5p # # modify so pdbs saved with lonepairs can be read back in # addPdbAtomMap { { "1EP+" "EP+1" } { "2EP+" "EP+2" } { "3EP+" "EP+3" } { "4EP+" "EP+4" } { "5EP+" "EP+5" } { "6EP+" "EP+6" } { "1EP-" "EP-1" } { "2EP-" "EP-2" } { "3EP-" "EP-3" } { "4EP-" "EP-4" } { "5EP-" "EP-5" } { "6EP-" "EP-6" } }