Hi Rashid,

Do let us know if it is protein-protein docking or protein-ligand docking?. In both cases, you need to narrow down to what kind of study you are going to perform. Same is the case with simulation too. You need to understand the biology behind your docking and simulations. There are excellent tools that can get these job done for you. However, these processes should be justified biologically.

Ok. Now im understand after some literature reading. Thanks a lot for give some advice.

Hi,

you can use Bevan Lab tutorial for MD simulation ligand-receptor complex.

if you've problems first see Bevan lab Lyzosime in water. if you haven't expertise in unix command, you can go for my tutorial of unix. Link: https://github.com/georopon