Seconding Dr. Case’s points, you can check out Phys. Chem. Chem. Phys., 2017, 19, 20593.
I think I used the parameters reported there when modeling the crystal structure of a protein with sulfates at the protein-protein interface.
Best,
Matthew
> On Jan 20, 2022, at 7:05 AM, David A Case <david.case.rutgers.edu> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> On Thu, Jan 20, 2022, zz sheng wrote:
>>
>> My protein-protein interface has a SO4, I wonder how to parameterize it for
>> MD? Could I use antechamber to generate the topology file and treat it as a
>> 'ligand'? I saw ions have different ways of parameterization in the manual.
>
> First, are you sure the sulphate is present under the conditions you are
> interested in? Unless you are simulating the crystal itself, that seems
> unlikely.
>
> Second, yes, antechamber will give you a good starting point. One could try
> to optimize those values based on experimental ion-water data. That is
> unlikely to make a big difference, and the choice depends on how important
> the sulphate is to your simulation.
>
> ....dac
>
>
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Received on Thu Jan 20 2022 - 05:00:03 PST
