Dear all,
We are working with a protein system with Mg2+ ions as metal cofactors in
the crystal structure. The activity of the protein is dependent on the
cofactor and has shown maximum deviation with Mn2+. We are trying to
capture the structural reasons for this using nanosecond classical MD
simulations. My query is regarding how we should replace the Mg2+ with
Mn2+. Is it okay to Manually edit the pdb from Mg to Mn and continue with
the parameter generation? Or do we need to take care of hydration or some
salt concentration set up while using Mn2+ (specific for Mn2+) ? TIP3P
automatically parameterized the Mg2+ ions, so is the same possible for Mn2+?
Kindly advise regarding the above matter.
Regards,
Sruthi Sudhakar
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Received on Sat Apr 16 2022 - 05:00:02 PDT
