On 4/03/2011 4:55 PM, Sunita Patel wrote:
Dear Users,
I performed MD simulation on a calcium binding protein with bound calcium
starting from the crystal structure using gromos96 forcefield with explicit
solvent with NVT ensembles. I performed energy minimization of calcium bound
protein with water and following this position restraint molecular dynamics
was performed. Subsequently, MD was performed on the system. In a less
than 100 ps the calcium ion diffuse away from protein. However, in the
experiment (NMR and X-ray)the protein is stable in calcium bound form.
What could be the reason for this?
Either your model does not provide a site that binds calcium, or you ran
into a periodicity effect (unlikely). Check the literature for
successful approaches for binding metal ions.
Mark
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