Re: [AMBER] Parameterize SO4

From: David A Case <>
Date: Thu, 20 Jan 2022 07:05:09 -0500

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

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.


AMBER mailing list
Received on Thu Jan 20 2022 - 04:30:03 PST
Custom Search