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

From: Chuck is Busy <>
Date: Sat, 13 Mar 2021 22:11:04 -0500

Hello David,

I believe the problem is the radii. I changed scnb and scee to try to get
different results.

The bond and the angle might be a little high, at 2125 and 5199
respectfully. I ran sander on a complex restrt file with mbondi set and I
have included the mdinfo. I visualized the simulation and tracked some
important distances, which looked fine to me.

On Sat, Mar 13, 2021 at 9:09 PM David A Case <> wrote:

> 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
> >sander?
> 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 - 19:30:02 PST
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