[AMBER] How to visualize the protein-implicit solvent boundary

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Thu, 5 Aug 2021 03:37:34 -0400

Dear Amber Community,

Is there a way to visualize the grid of points where the implicit solvent is being evaluated?

I am running constant pH and redox simulations, and I suspect that one of the redox potentials is significantly wrong (too negative) because the implicit dielectric is being placed where it ought not go. If I let all pH and redox active groups be titratable, the redox potentials for two of the three heme cofactors in my system come within 5 meV of the experimental values, which themselves have a 5 meV error bar. The third heme, however, has a redox potential that is more negative compare to experiment by ~150 meV (absolute value = -266 meV).

Even if there is nothing I can do to remedy the discrepancy, I would still like to assess by some means if this hypothesis is right, or if something else is amiss.

Best regards,
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Received on Thu Aug 05 2021 - 01:00:02 PDT
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