I made homology models for a set of proteins and want to compare the hydrogen bonding network around the active sites. For this I would like to place water molecules in the channels and pores around the active site. Do you know a simple software that can place the water molecules without doing an MD simulation?
You can try PDB_HYDRO server (http://lorentz.dynstr.pasteur.fr/pdb_hydro.php). It does some basic minimization after adding the waters but I don't think it'll optimize the hydrogen bonding network. So, in addition to this, you can try protein preparation wizard of Free Maestro, where you can sample the orientations of water molecules to optimize the hydrogen bond network without running MD. I personally do not recommend this, though. I would go for at least short restrained MD.
You could at least go to till the energy minimization step of MD and do it for 1-5 ns, at the very least.
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