[AMBER] Initial configuration of ADP and ion simulation using AMBER.

From: Abhilash J <md.scfbio.gmail.com>
Date: Thu, 31 May 2018 22:15:12 +0530

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.


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Received on Thu May 31 2018 - 10:00:01 PDT
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