Re: [AMBER] MMGBSA calculations - mbondi parameter

From: David A Case via AMBER <>
Date: Mon, 16 Jan 2023 13:32:10 -0500

On Mon, Jan 16, 2023, Maria Bzwka via AMBER wrote:

>I performed the MD simulation of the protein-ligand complex and now I want
>to run the MMGBSA calculations. However, in the .prmtop file that I
>prepared for MD simulation, I didn't specify the radii parameter. Using
> script I created the complex, receptor and ligand topology
>files (including radii parameter) but now I'm thinking that the results may
>be inconsistent regarding the topology of the solvated complex (where the
>radii is not specified).

As Carlos noted, you don't need to re-run any explicit solvent simulations,
since they don't use radii.

You do need radii for MMGBSA calculations. You can use parmed to check, and
to modify, the radii sets that are in the prmtop files that
creates. But I think(?) the defaults that you get are usually what you


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Received on Mon Jan 16 2023 - 11:00:03 PST
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