Dear All,

I have modelled a membrane protein and a globular protein and docked them with few natural compounds that we identified. after docking, I thought of simulating both the protein complexes.

1) The membrane protein could not be simulated in desmond, so I am trying discovery studio for it.( Due to time and computational facility limitation, I cannot cary out gromacs) 2)For the globular protein I am currently running dynamics using desmond for 5 ns.

My query is : 1) will a question arise as to why I chose to do simulation using 2 different packages? 2) for both the proteins glide docking with OPLS2005 force field was carried out. but now for simulation of membrane protein, if I use discovery studio that has charmm as the force field, is my methodology wrong? if I carry out simulation in Discovery studio how can I justify it?

kindly suggest

regards lavanya