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 dna.ac -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 DAP.ac -o DAP.prepi -f prepi -m mainchain.pro4 -rn DAP -rf ""
prepgen -i DCP.ac -o DCP.prepi -f prepi -m mainchain.pro4 -rn DCP -rf ""
prepgen -i DGP.ac -o DGP.prepi -f prepi -m mainchain.pro4 -rn DGP -rf ""
prepgen -i DTP.ac -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
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