See the tutorial of NAMD

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/

http://www.ks.uiuc.edu/Training/Tutorials/

and user's guide

http://www.ks.uiuc.edu/Research/namd/2.12/ug/

Hi, you can search in NAMD tutorials (psf, pdb, ...)

Dear Vineeta,

we add ions with VMD plugin called autoionize . you can manipulate its script. you can consider GuHCl just like NaCl but urea like a single ion and replace it with NA for instance.

Bests

Farzane