[gmx-users] Metal-Protein interactions
drrahulsuresh at gmail.com
Tue Nov 28 10:54:03 CET 2017
I am trying to simulate a metal-protein interaction using gromacs 2016
package and charmm36 ff.
I have prepared the initial pdb by performing an oniom calculations between
protein and metal (at various positions) using gaussian 09 and chose the
structure with maximum binding energy. The metal ion is bonded to oxygen
atom of His residue. Having a look at gro file after each step
(protein.gro, em.gro, nvt.groand npt.gro) the distance between metal ion
and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over the
course of simulations for 10ns, the metal ion is away from the protein.
What can be done to have the metal ion restrained at its position? Or if I
extend the simulation will the metal ion find its appropritae position
during the course time?
Sounds dramatic I guess, but still that remains in my mind.
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