Hello experts,
I used ChemSketch to draw DNA with the presence of probe at the 5' terminal. Later, I convert the Sketch to .sdf and .sdf to .pdb using Discovery Studio. However, when I visualized the output, the DNA looks 'rigid' (picture attached) and the naming & numbering of DNA in pdb file generated from ChemSketch is 'weird' (pdb file attached)..
I'm just wondering is there any other software that can integrate/combine the nucleic acid with chemical structure (probe etc.) as 1 entity (in pdb file format), specifically at 5' or 3' for in silico study?
TQ in advance :)