Re: [AMBER] MMGBSA calculations - mbondi parameter

From: Maria Bzówka via AMBER <>
Date: Thu, 19 Jan 2023 10:04:57 +0100

Thanks for the comment, I took care of it.


On Mon, 16 Jan 2023 at 19:32, David A Case <> wrote:

> On Mon, Jan 16, 2023, Maria Bzówka 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
> want.
> ....dac
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Received on Thu Jan 19 2023 - 01:30:03 PST
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