We will simulate a B-type DNA octamer using AMBER. In the first step, we will create the prmtop and rst7 files. In this video, we have used xleap to generate the files. The initial structure of the DNA molecule can be created using NAB.
Yes, you can create the prmtop and rst7 files of the complexes. But first you have to generate the modified forcefield parameters of the ligand/small molecule using Antechamber.
Thank for your tutorial! sir i have a DNA + protein duplex in this case what I do using force field? source leaprc ff19SB (protein) source leaprc water.opc or source leaprc ff19SB source leaprc.DNA.OL15 source leaprc water.opc
@@mdwithgourav9263 Thank you sir ! I have one more question. In my case DNA + protein pdb Does the protein force field affect dna in Amber? The opposite is the case (whether the dna force field affects the protein?) I want to know if the force field applies individually.
