topology top_all27_na.rtf
topology top_all22_prot.inp
alias residue HIE HSD
alias atom ARG H HN  
alias atom ARG H1 HT1
alias atom ARG H2 HT2
alias atom ARG H3 HT3
alias atom ARG 2HB HB1
alias atom ARG 3HB HB2
alias atom ARG 2HG HG1
alias atom ARG 3HG HG2
alias atom ARG 2HD HD1
alias atom ARG 3HD HD2
alias atom ARG 1HH1 HH11
alias atom ARG 2HH1 HH12
alias atom ARG 1HH2 HH21
alias atom ARG 2HH2 HH22
alias atom LYS H HN
alias atom LYS 2HB HB1
alias atom LYS 3HB HB2
alias atom LYS 2HG HG1
alias atom LYS 3HG HG2
alias atom LYS 2HD HD1
alias atom LYS 3HD HD2
alias atom LYS 2HE HE1
alias atom LYS 3HE HE2
alias atom LYS 1HZ HZ1
alias atom LYS 2HZ HZ2
alias atom LYS 3HZ HZ3 
alias atom GLN H HN
alias atom GLN 2HB HB1
alias atom GLN 3HB HB2
alias atom GLN 2HG HG1
alias atom GLN 3HG HG2
alias atom GLN 1HE2 HE21
alias atom GLN 2HE2 HE22
alias atom ALA H HN
alias atom ALA 1HB HB1
alias atom ALA 2HB HB2
alias atom ALA 3HB HB3
alias atom TRP H HN
alias atom TRP 2HB HB1
alias atom TRP 3HB HB2
alias atom LEU H HN
alias atom LEU 2HB HB1
alias atom LEU 3HB HB2
alias atom LEU 1HD1 HD11
alias atom LEU 2HD1 HD12
alias atom LEU 3HD1 HD13
alias atom LEU 1HD2 HD21
alias atom LEU 2HD2 HD22
alias atom LEU 3HD2 HD23
alias atom GLU H HN
alias atom GLU 2HB HB1
alias atom GLU 3HB HB2
alias atom GLU 2HG HG1
alias atom GLU 3HG HG2
alias atom ASP H HN
alias atom ASP 2HB HB1
alias atom ASP 3HB HB2
alias atom ASN H HN
alias atom ASN 2HB HB1
alias atom ASN 3HB HB2
alias atom ASN 1HD2 HD21
alias atom ASN 2HD2 HD22
alias atom SER H HN
alias atom SER 2HB HB1
alias atom SER 3HB HB2
alias atom SER HG HG1
alias atom SER O1 OT1
alias atom SER O2 OT1
alias atom GLY H HN
alias atom GLY 2HA HA1
alias atom GLY 3HA HA2
alias atom VAL H HN
alias atom VAL 1HG1 HG11
alias atom VAL 2HG1 HG12
alias atom VAL 3HG1 HG13
alias atom VAL 1HG2 HG21
alias atom VAL 2HG2 HG22
alias atom VAL 3HG2 HG23
alias atom TYR H HN
alias atom TYR 2HB HB1
alias atom TYR 3HB HB2
alias atom ILE H HN
alias atom ILE 1HG2 HG21
alias atom ILE 2HG2 HG22
alias atom ILE 3HG2 HG23
alias atom ILE 2HG1 HG11
alias atom ILE 3HG1 HG12
alias atom ILE CD1 CD
alias atom ILE 1HD1 HD1
alias atom ILE 2HD1 HD2
alias atom ILE 3HD1 HD3
alias atom HIE H HN
alias atom HIE 2HB HB1
alias atom HIE 3HB HB2
alias atom PHE H HN
alias atom PHE 2HB HB1
alias atom PHE 3HB HB2
alias atom THR H HN
alias atom THR 1HG2 HG21
alias atom THR 2HG2 HG22
alias atom THR 3HG2 HG23
alias atom THR 1HG HG1
alias atom MET H HN
alias atom MET 2HB HB1
alias atom MET 3HB HB2
alias atom MET 2HG HG1
alias atom MET 3HG HG2
alias atom MET 1HE HE1
alias atom MET 2HE HE2
alias atom MET 3HE HE3
alias residue DG5 GUA
alias residue DG3 GUA
alias residue DC5 CYT
alias residue DC3 CYT
alias residue DA ADE
alias residue DT THY
alias residue DG GUA
alias residue DC CYT
alias atom DG 1H2' H2'
alias atom DG 2H2' H2''
alias atom DG 1H5' H5'
alias atom DG 2H5' H5''
alias atom DG 1H2 H21
alias atom DG 2H2 H22
alias atom DG5 1H2' H2'
alias atom DG5 2H2' H2''
alias atom DG5 1H5' H5'
alias atom DG5 2H5' H5''
alias atom DG5 1H2 H21
alias atom DG5 2H2 H22
alias atom DG3 1H2' H2'
alias atom DG3 2H2' H2''
alias atom DG3 1H5' H5'
alias atom DG3 2H5' H5''
alias atom DG3 1H2 H21
alias atom DG3 2H2 H22
alias atom DA 1H2' H2'
alias atom DA 2H2' H2''
alias atom DA 1H5' H5'
alias atom DA 2H5' H5''
alias atom DA 1H6 H61
alias atom DA 2H6 H62
alias atom DT 1H2' H2'
alias atom DT 2H2' H2''
alias atom DT 1H5' H5'
alias atom DT 2H5' H5''
alias atom DT C7 C5M
alias atom DT 1H7 H51
alias atom DT 2H7 H52
alias atom DT 3H7 H53
alias atom DC 1H2' H2'
alias atom DC 2H2' H2''
alias atom DC 1H5' H5'
alias atom DC 2H5' H5''
alias atom DC 1H4 H41
alias atom DC 2H4 H42
alias atom DC5 1H2' H2'
alias atom DC5 2H2' H2''
alias atom DC5 1H5' H5'
alias atom DC5 2H5' H5''
alias atom DC5 1H4 H41
alias atom DC5 2H4 H42
alias atom DC3 1H2' H2'
alias atom DC3 2H2' H2''
alias atom DC5 1H5' H5'
alias atom DC5 2H5' H5''
alias atom DC5 1H4 H41
alias atom DC5 2H4 H42
alias residue HOH TIP3
alias atom HOH OW OH2
alias atom HOH HW1 H1
alias atom HOH HW2 H2 
delatom atom DG5 O2'
delatom atom DG O2'
delatom atom DG5 O2'
delatom atom DG3 O2'
delatom atom DA O2'
delatom atom DT O2'
delatom atom DG O2'
delatom atom DC O2'
delatom atom DC5 O2'
delatom atom DC3 O2'
segment 1IV6 {
         pdb protein.pdb
}
coordpdb protein.pdb 1IV6
segment DNA {
         pdb DNA.pdb
}
patch DEO2 DNA:58
patch DEO1 DNA:59
patch DEO1 DNA:60
patch DEO2 DNA:61
patch DEO2 DNA:62
patch DEO2 DNA:63
patch DEO2 DNA:64
patch DEO1 DNA:65
patch DEO1 DNA:66
patch DEO2 DNA:67
patch DEO2 DNA:68
patch DEO2 DNA:69
patch DEO2 DNA:70
patch 5TER DNA:58
patch 3TER DNA:70
patch DEO1 DNA:71
patch DEO1 DNA:72
patch DEO1 DNA:73
patch DEO1 DNA:74
patch DEO2 DNA:75
patch DEO2 DNA:76
patch DEO1 DNA:77
patch DEO1 DNA:78
patch DEO1 DNA:79
patch DEO1 DNA:80
patch DEO2 DNA:81
patch DEO2 DNA:82
patch DEO1 DNA:83
patch 5TER DNA:71
patch 3TER DNA:83
coordpdb DNA.pdb DNA
segment WAT {
          pdb  water_b.pdb
}
coordpdb water_b.pdb WAT
segment  SOD {
          pdb NA_ION.pdb
}
coordpdb NA_ION.pdb SOD
writepdb pro_dna_ion_wat.pdb
writepsf pro_dna_ion_wat.psf