[gtkleap]$ source leaprc.ff99SB
logFile leap.log
#
# ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
# -----  this file is updated for PDB format 3
#
#	load atom type hybridizations
#
addAtomTypes {
	{ "H"   "H" "sp3" }
	{ "HO"  "H" "sp3" }
	{ "HS"  "H" "sp3" }
	{ "H1"  "H" "sp3" }
	{ "H2"  "H" "sp3" }
	{ "H3"  "H" "sp3" }
	{ "H4"  "H" "sp3" }
	{ "H5"  "H" "sp3" }
	{ "HW"  "H" "sp3" }
	{ "HC"  "H" "sp3" }
	{ "HA"  "H" "sp3" }
	{ "HP"  "H" "sp3" }
	{ "OH"  "O" "sp3" }
	{ "OS"  "O" "sp3" }
	{ "O"   "O" "sp2" }
	{ "O2"  "O" "sp2" }
	{ "OW"  "O" "sp3" }
	{ "CT"  "C" "sp3" }
	{ "CH"  "C" "sp3" }
	{ "C2"  "C" "sp3" }
	{ "C3"  "C" "sp3" }
	{ "C"   "C" "sp2" }
	{ "C*"  "C" "sp2" }
	{ "CA"  "C" "sp2" }
	{ "CB"  "C" "sp2" }
	{ "CC"  "C" "sp2" }
	{ "CN"  "C" "sp2" }
	{ "CM"  "C" "sp2" }
	{ "CK"  "C" "sp2" }
	{ "CQ"  "C" "sp2" }
	{ "CD"  "C" "sp2" }
	{ "CE"  "C" "sp2" }
	{ "CF"  "C" "sp2" }
	{ "CP"  "C" "sp2" }
	{ "CI"  "C" "sp2" }
	{ "CJ"  "C" "sp2" }
	{ "CW"  "C" "sp2" }
	{ "CV"  "C" "sp2" }
	{ "CR"  "C" "sp2" }
	{ "CA"  "C" "sp2" }
	{ "CY"  "C" "sp2" }
	{ "C0"  "C" "sp2" }
	{ "MG"  "Mg" "sp3" }
	{ "N"   "N" "sp2" }
	{ "NA"  "N" "sp2" }
	{ "N2"  "N" "sp2" }
	{ "N*"  "N" "sp2" }
	{ "NP"  "N" "sp2" }
	{ "NQ"  "N" "sp2" }
	{ "NB"  "N" "sp2" }
	{ "NC"  "N" "sp2" }
	{ "NT"  "N" "sp3" }
	{ "N3"  "N" "sp3" }
	{ "S"   "S" "sp3" }
	{ "SH"  "S" "sp3" }
	{ "P"   "P" "sp3" }
	{ "LP"  ""  "sp3" }
	{ "F"   "F" "sp3" }
	{ "CL"  "Cl" "sp3" }
	{ "BR"  "Br" "sp3" }
	{ "I"   "I"  "sp3" }
	{ "FE"  "Fe" "sp3" }
	{ "EP"  ""  "sp3" }
# glycam
	{ "OG"  "O" "sp3" }
	{ "OL"  "O" "sp3" }
	{ "AC"  "C" "sp3" }
	{ "EC"  "C" "sp3" }
}
#
#	Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
#
#	Load DNA/RNA libraries
#
loadOff all_nucleic94.lib
#
#	Load main chain and terminating 
#	amino acid libraries (i.e. ff94 libs)
#
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
#
#       Load water and ions
# 
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#
#	Define the PDB name map for the amino acids and DNA.
#
addPdbResMap {
  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
  { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
  { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
  { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
  { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
  { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
  { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
  { 0 "SER" "NSER" } { 1 "SER" "CSER" }
  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
  { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
  { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
  { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
  { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
  { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
  { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
  { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
  { 0 "G" "RG5"  } { 1 "G" "RG3"  } { "G" "RG" } { "GN" "RGN" }
  { 0 "A" "RA5"  } { 1 "A" "RA3"  } { "A" "RA" } { "AN" "RAN" }
  { 0 "C" "RC5"  } { 1 "C" "RC3"  } { "C" "RC" } { "CN" "RCN" }
  { 0 "U" "RU5"  } { 1 "U" "RU3"  } { "U" "RU" } { "UN" "RUN" }
  { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }  
  { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }  
  { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }  
  { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }
}
addPdbAtomMap {
  { "O5*" "O5'" }
  { "C5*" "C5'" }
  { "C4*" "C4'" }
  { "O4*" "O4'" }
  { "C3*" "C3'" }
  { "O3*" "O3'" }
  { "C2*" "C2'" }
  { "C1*" "C1'" }
  { "C5M" "C7"  }
  { "O2*" "O2'" }
  { "H1*" "H1'" }
  { "H2*1" "H2'1" }
  { "H2*2" "H2'2" }
  { "H2'"  "H2'1" }
  { "H2''" "H2'2" }
  { "H3*" "H3'" }
  { "H4*" "H4'" }
  { "H5*1" "H5'1" }
  { "H5*2" "H5'2" }
  { "H5'"  "H5'1" }
  { "H5''" "H5'2" }
  { "HO2'" "HO'2" }
  { "HO5'" "H5T" }
  { "HO3'" "H3T" }
  { "O1'" "O4'" }
  { "OA"  "O1P" }
  { "OB"  "O2P" }
  { "OP1" "O1P" }
  { "OP2" "O2P" }
}
#
# assumed that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
[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_06g.dat
Info: ignoring unknown atom type: NH
Info: while reading DIHE. Input: NH CG CG SM   1    0.45          0.0             3.         SCEE=1.0 SCNB=1.0 Thiol linkages
Info: ignoring unknown atom type: NP
Info: ignoring unknown atom type: NO
Info: ignoring unknown atom type: CX
##
#
#       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]$ set default write14scale on
[gtkleap]$ com = loadpdb PRA_crd1.pdb
make bond between atom 206 378
[gtkleap]$ bond com.111.O1 com.112.C1
[gtkleap]$ bond com.112.O3 com.113.C1
[gtkleap]$ bond com.112.O6 com.114.C1
[gtkleap]$ solvateOct com TIP3PBOX 12.0
rgn size:    73.137    73.137    73.137
svt size:    18.774    18.774    18.774
nx,ny,nz: 4 4 4
[gtkleap]$ charge com
3
[gtkleap]$ addions com Cl- 0
Info: solute natom, total natom: 1727 17621
      solute nresd, total nresd: 114 5412
Info: rmax, rion, shell: 2 2.47 4
Info: pmin: -17.1928 -18.4543 -19.3943
Info: pmax: 18.819 19.1759 17.4917
Info: enclosing: -25.6628 -26.9243 -27.8643
Info:        to: 27.289 27.6459 25.9617
Info: looking for bump solvent near: -0.66278 16.0757 7.13572
Info: bump with -2.36632 17.6452 6.95418
Info: looking for bump solvent near: 7.33722 13.0757 9.13572
Info: bump with 9.07185 14.1278 10.8775
Info: looking for bump solvent near: -6.66278 9.0757 6.13572
Info: bump with -6.41611 10.8234 6.87752
[gtkleap]$ saveamberparm com pra_crd1_solvated.prmtop pra_crd1_solvated.inpcrd
[gtkleap]$ quit