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Answer from @pippo1980, converted from comment: https://pubs.acs.org/doi/10.1021/acs.jctc.9b01208 Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes


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Answer from @matteo-ferla, converted from comment: If command line interface is more suitable for you, you may consider OpenBabel, which can predict Gasteiger charges, protonate at pH 7, accept a smi file of multiple SMILES or a multi-entry sdf file and can output in PDQBT format, but is not quite the same as the python script allows merging and various ...


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I regularly use the site you cited (scfbio...) to generate idealized straight DNA segments for illustration purposes. It is not sequence-dependent. For an actual solved structure you can extract specific chains from existing structures containing DNA (e.g. RNA polymerase II structures by the Cramer group). These structures will have their own sequence, not ...


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the tutorials video on youtube Gromacs has great written documentation, so I'd suggest referring to that directly. I can also use GROMACS if that gives me the results. Gromacs works fine with a DNA-ligand system. There are different Amber forcefields, proteins are generally used with AMBER99SB-ILDN simply because it has the longest name and is one of the ...


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