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 mail your suggestions as early as possible to {deleted}
regards lavanya
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