[gmx-users] protein-ligand complex

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Thu Jan 16 15:59:56 CET 2014

hi GMX user
please help me

i want to simulated a protein-ligand complex. This complex has previously been studied experimentally. I  draw and opt this ligand by Gaussian software. i get the native protein of RCSB. i dock my ligand in the active site of the protein and select the best pose. 
This pose was almost close to the experimental structure, but not much. i run 10ns simulation but the simulation results were not close to the experimental results, especially conformation of the ligand in the active site of the protein.

I sincerely request your help.
thanks a lot

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