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 - 04:30:03 PST
