Find the edited PDB on the desktop
Need to include all the sections of the simulation including all the different proteins or peptides or drugs or any other missing molecules
Then upload to the CHARMM-
GUI PDB reader
Be sure to keep certain options like the terminal group patching consistent
Be sure to preserve any disulfide bonds… check everything
On the appropriate screen select “rename” to rename the different components to the original names
Check that all the components are there after this step and download the contents
Upload the *.pdb, *.psf, *.crd, *.str, and copy the NAMD toppar folder from the original simulation and place in a new folder
Then follow the instructions on the NAMD 1D PMF to restart the simulation from a set of given *psf, *pdb …
Edit the *.str to mimic many of the lines from the old simulation's *str since this *.str was written for CHARMM and we're using NAMD
Use the Xmin and Xmax, Ymin… to get the lengths of the different axis
Update the number of waters now that it has been adjusted