On Sat, Apr 16, 2022, Sruthi Sudhakar wrote:
>
>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+?
The leaprc.water.xxx files load both the water model, and monatomic ions
that are compatible with that model. So, operationally, you should be able
to substitute MN for MG in an input pdb file, and LEaP will find the
parameters. Whether or not a short classical MD simulation will explain the
activity difference is a separate question.
...dac
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Received on Sat Apr 16 2022 - 05:00:02 PDT
