Autodock put zero total charge to Cuisaepy. So, the ligand has zro charge and Cu ion has zero charge. I changed by hand the charge of Cu as +1.
The initial docking position was in minor groove with Cu poiting to DNA
The docking results shows an inverted Cuisaepy position with Cu pointing to the outside of the DNA. This because the Cu is highly charged in comparision to the rest of the ligand. So I'll include the resp charges
1) check pdb for DNA+metal-complex
I didn't find it
2) Run resp charges using gaussian
3) Run intercalating complex
/mgltools_x86_64Linux2_1.5.6/bin/pythonsh /mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r DNA.mol2 -C -U lps -o DNAwh.pdbqt
#/mgltools_x86_64Linux2_1.5.6/bin/pythonsh /mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r DNA.mol2 -C -U lps -o DNAwh.pdbqt
/mgltools_x86_64Linux2_1.5.6/bin/pythonsh /mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l cie.mol2 -C -p Cu -U lps -o CIEwh.pdbqt
vina --config conf_isaepy.txt --log vina.log
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