[AMBER] MMGBSA calculations - mbondi parameter

From: Maria Bzówka via AMBER <amber.ambermd.org>
Date: Mon, 16 Jan 2023 15:16:20 +0100

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
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Received on Mon Jan 16 2023 - 06:30:02 PST
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