I am actually new to this sort of molecular modelling. I am trying to insert
a protein into a cnt, and then run some simulations. I have the protein and
cnt .pdb files, but am not able to understand which program to use to
combine them together, and get a visual picture, so that I can be sure that
the protein fits properly. I tried vmd, however it seems vmd only gives a
visual picture, however doesn't exactly change the molecular coordinates.
Could you kindly inform me as to which software I could use for such a job?