Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI

From: David A Case <>
Date: Sat, 13 Mar 2021 21:08:48 -0500

On Sat, Mar 13, 2021, Chuck is Busy wrote:
>If my simulation was run without defining a radii, what radii or what
>values can I set for my 3 topology files to get reasonable values with

Are you sure the MMPBSA "problems" arise from the radii? In you earlier
post, you said that you changed the values of scnb and scee as well. It's
worth checking that.

If you are getting deltaG values of around 1500 kcal/mol, look carefully at
the details of the outputs: are there any components of the energies that
look odd? Have you tried the "single trajectory" approach to see if that
gives different values? Being off by thousands of kcal/mol seems like
something that you ought to be able to track down. If you haven't already
done so, be sure to visualize the trajectories, and do the free energy
calculations "by hand", i.e. without relying on MMPBSA.

....good luck....dac

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Received on Sat Mar 13 2021 - 18:30:02 PST
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