I would like to know any steps one needs to follow for generating PDB file for their custom dsDNA sequence. I am working on drug-DNA intercalation but the dsDNA sequence is not very long and it is custom designed so I cannot download PDB file for it from the data bank.
I did went through some old questions where some are suggesting to use chimera where others are against it. What suggestions or thoughts do you have on generating/creating your own pdb file. Can we trust those files the way we trust the file from protein data bank?