leapscript.txt

source leaprc.protein.ff14SB
source leaprc.gaff
addAtomTypes {
	{ "M1" "Fe" "sp3" }
        { "Y1" "N"  "sp3" } 
        { "Y2" "N"  "sp3" }
        { "Y3" "N"  "sp3" }
        { "Y4" "N"  "sp3" }
        { "Y5" "O"  "sp3" }
        { "Y6" "O"  "sp3" }
}
addAtomTypes{
        { "o"  "O"  "sp3" }
        { "c2" "C"  "sp2" }
        { "c3" "C"  "sp3" }
        { "ha" "H"  "sp3" }
        { "hb" "H"  "sp3" }
}
HD1 = loadmol2 HID250.mol2
HD2 = loadmol2 HID255.mol2
HD3 = loadmol2 HID430.mol2
HE1 = loadmol2 HIE434.mol2
IE1 = loadmol2 ILE552.mol2
OH1 = loadmol2 OH.mol2
FE2 = loadmol2 FE2.mol2
HXA = loadmol2 HXA.mol2
loadAmberParams OH.frcmod
loadAmberParams frcmod.ionsjc_tip3p
loadAmberParams centre_actiu.frcmod
loadAmberParams HXA.frcmod 
prot = loadPdb 20-II--1bis-3rde_A_HXA_millor_docking_final.pdb
bond prot.250.NE2 prot.554.FE
bond prot.255.NE2 prot.554.FE
bond prot.430.NE2 prot.554.FE
bond prot.434.ND1 prot.554.FE
bond prot.552.OXT prot.554.FE
bond prot.553.O1  prot.554.FE
bond prot.249.C   prot.250.N
bond prot.250.C   prot.251.N
bond prot.254.C   prot.255.N
bond prot.255.C   prot.256.N
bond prot.429.C   prot.430.N
bond prot.430.C   prot.431.N
bond prot.433.C   prot.434.N
bond prot.434.C   prot.435.N
bond prot.551.C   prot.552.N   
savePdb prot 20-II--1-3rde_A_HXA_tleap_dry.pdb
saveAmberParm prot 20-II--1-3rde_A_HXA_tleap_dry.prmtop 20-II--1-3rde_A_HXA_tleap_dry.inpcrd
source leaprc.water.tip3p
solvateBox prot TIP3PBOX 10.0
addIons prot Na+ 0 
addIons prot Cl- 0
savePdb prot 20-II--1-3rde_A_HXA_tleap_solvatat_ion.pdb
saveAmberParm prot 20-II--1-3rde_A_HXA_tleap_solvatat_ion.prmtop 20-II--1-3rde_A_HXA_tleap_solvatat_ion.inpcrd
quit