Re: [AMBER] pbsa question

From: Jason Swails <>
Date: Mon, 12 Jan 2015 11:41:44 -0500

> On Jan 12, 2015, at 11:25 AM, zahra khatti <> wrote:
> For example for visualizing electrostatic potential map in vmd,I didn't see any option in; but there is in pbsa.

But you had said you wanted to plot van der Waals and binding free energies -- those can be done with (well, not the plotting part). This option is unrelated to your original question as far as I can tell?

I’m not sure what question you are trying to ask here: if doesn’t do something you want, you can’t use it for that. If it does do what you want, you can use it. Same goes for PBSA (or any other Amber program).

A general rule of thumb is that if something doesn’t relate directly to calculating energies, is probably not the right tool.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 12 2015 - 09:00:03 PST
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