Hello amber users,
I´m trying to run a MD simulation of a carbohydrate-protein complex in which
the interaction is Ca2+ dependent. Specifically, the Ca2+ ion is coordinated
to 2 OH groups of the non reducing end
sugar residue. I´m using the crystal structure as the starting structure and
I´m also using explicit solvent. However, after a pair of ns of the
production dynamics THE LIGAND loses its coordination
with Ca2+ (IMPORTANT: CA2+ keeps its original position in the binding site).
I should also highlight that the ligand does not move apart from the binding
area, just lose its Ca2+ coordination, so
its original binding mode. Is there any strategy from the computational side
to overcome this issue? Is it actually the MD technique powerful enough to
study this kind of transient and weak interaction
or would it be necessary to use QM/MM?
Thank you very much.
Best regards.
Juan Carlos Muñoz García.
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Received on Wed Nov 23 2011 - 04:30:02 PST
