Yeah, one can use NAMD to run simulations on protein-ligand complexes if he has good set of force field parameters.

Suresh Gorle

Sir can you tell me how can i get topology and parameters for protein to be run in NAMD>?> I know for ligand but i don't know how to get for Protein.

Could you be more specific about the force field you are planning to use? For CHARMM force field, you can download the parameters from Prof.Alex Mackerell website (http://mackerell.umaryland.edu/CHARMM_ff_params.html). You can use those parameters directly in NAMD. In case AMBER force field, you can download AMBER force field and required AMBER tools from http://ambermd.org/. You can prepare input files using AMBER tools that can be used directly in NAMD. In the case of CHARMM force field, you can use VMD program to generate input files which can be used directly in NAMD to run molecular dynamics simulations. There are plenty of tutorials available in online (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node4.html). 

i want to use AMBER FF. 

you can find the AMBER FF parameters for proteins the weblink I had specified before. Use amber tools and prepare the initial files like adding waterbox, adding ions. These output files can use directly in NAMD to run MD simulations. see this link: http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html