Re: [AMBER] Parameterize SO4

From: Matthew Guberman-Pfeffer <>
Date: Thu, 20 Jan 2022 07:50:00 -0500

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.


> On Jan 20, 2022, at 7:05 AM, David A Case <> 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
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