Generate Topology File For Nucleotide With The Phosphate Group Protonated

  • Step 1:
    Prepare a model molecule: dna.jpg
  • Step 2:
    Generate a gaussian input file: dna.gau from a mol2 file dna.mol2
    antechamber -fi mol2 -fo gzmat -i dna.mol2 -o dna.gau
  • Step 3:
    Run gaussian to get the output file: alpha
  • Step 4:
    Run antechamber to get some intermediate files for further modification
    antechamber -fi gout -fo ac -i dna.mol2 -o -c resp
    There are a couple of intermediate files generated: ANTECHAMBER.ESP, ANTECHAMBER_RESP1.IN, ANTECHAMBER_RESP2.IN etc. Rename ANTECHAMBER.ESP to dna.esp ; rename ANTECHAMBER_RESP1.IN to dna-step1.respin and ANTECHAMBER_RESP2.IN to dna-step2.respin. Manually modify the two RESP input files to add charge constraint:
    qO7 = -0.5232 (O3')
    qO28 = -0.4954 (O5')
    qH14 + qP29 + qO28 + qO31 = 0.6137

    The following is the finally input files for the two-stage RESP fitting: Stage I and Stage II
    Run the following command to generate resp charges:
    resp -O -i dna-step1.respin -o dna-step1.respout -e dna.esp -t dna-step1.crg
    resp -O -i dna-step2.respin -o dna-step2.respout -e dna.esp -q dna-step1.crg -t dna-step2.crg
    The following is the output files for the two-stage RESP fitting: Stage I and Stage II ; the final charges for qH14, qP29, qO28 and qO31 are 0.4333, 1.7381, -0.8266 and -0.7311, respectively.
  • Step 5:
    Prepare ac files for those nucleotides (DAP, DCP, DGP, DTP)
  • Step 6:
    Read in ac files and a mainchain defination file mainchain.dna to generate prep input file (DAP, DCP, DGP, DTP) by using prepgen
    In mainchain defination file, HEAD_NAME is the atom connected to the immediately previous residue and TAIL_NAME is the atom connected to the immediately behide reside; MAINCHAIN are mainchain atoms (HEAD_NAME and TAIL_NAME are mainchain atoms automatically, but should not be defined explicitly);
    prepgen -i -o DAP.prepi -f prepi -m mainchain.pro4 -rn DAP -rf  ""
    prepgen -i -o DCP.prepi -f prepi -m mainchain.pro4 -rn DCP -rf  ""
    prepgen -i -o DGP.prepi -f prepi -m mainchain.pro4 -rn DGP -rf  ""
    prepgen -i -o DTP.prepi -f prepi -m mainchain.pro4 -rn DTP -rf  ""

    Similar procedure is used to generate topology files for DA3P, DC3P, DG3P and DT3P.
  • Step 7:
    With those residue topologies, one may use leap to generate topolgy files for molecular mechanical calculations. Here we generate a topology file for DG5-DGP-DGP-DGP-DGP3 with xleap.
    loadamberprep DGP.prepi
    loadamberprep DGP3.prepi
    aa =sequence {DG5 DGP DGP DGP DGP3}
    saveamberparm aa dna_example.prmtop dna_expample.prmcrd