if you ran the original MD with explicit solvent, the "pbradii" from the
prmtop were not used for that part.
On Mon, Jan 16, 2023 at 9:17 AM Maria Bzówka via AMBER <amber.ambermd.org>
wrote:
> Dear Amber Users,
>
> 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
> ante-MMPBSA.py 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).
>
> Should I repeat the preparation of the .prmtop file and run the simulation
> once again?
>
> Thank you in advance
> Maria
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Received on Mon Jan 16 2023 - 06:30:03 PST
