Thank you for the quick reply. Do we need to do any other changes specific
to simulations with Mn2+? I have not come across anything in literature so
far. If there is something kindly comment on the same.
Regards,
Sruthi
On Sat, 16 Apr 2022 at 5:26 PM, David A Case <david.case.rutgers.edu> wrote:
> 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 - 05:30:02 PDT
