Hi everyone,
I plan on simulating a ADP with one MG2+ion and protein.
Will it be plausible to take a Mg2+ with 6 co-ordinate bonds. Three with
Oxygen atoms of ADP (in the phosphates) and three with oxygen atoms in
water molecules (Octahedral form).
I can parameterize this using MCPB.py or Gaussian to get a bonded or a
non bonded model to run simulation in it.
I don't want to keep bonds with the protein as i need to study the
dissociation of ADP from the protein.
Is the ADP + MG2 + 3 water in Octahedral form configuration a reasonable
assumption for a starting structure.
Regards
Abhilash
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Received on Thu May 31 2018 - 10:00:01 PDT
