logFile leap.log # # ----- leaprc for loading the glycam04EP force field, with lone pairs # with sp2 lone pairs of 0.45A and sp3 lone pairs 0.70A # no lone pairs on carboxyalte groups # # 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" } { "EP" "" "sp3" } } # ################# PLEASE NOTE ######################## ## ## Updated copies of the GLYCAM parameter and ## prep files can be downloaded from the GLYCAM ## web site's Documentation page. The current ## location of the page (on 20060515) is: ## ## http://legacy.glycam.org/gl_params.html ## ####################################################### # # load the main paramter set # glycam04EP = loadamberparams Glycam_04EP.dat # # load all prep files for polysaccharides including lone pairs # loadamberprep Glycam_04EP.prep # # # 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 # HOH = TP3 WAT = TP3 # # # 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" } }