Re: [AMBER] the better box size for calculating host-guest interaction energies

From: Jason Swails <>
Date: Thu, 20 Aug 2015 10:32:34 -0400

On Thu, 2015-08-20 at 10:09 -0400, Investigador QuĂ­mica wrote:
> Dear Jason, thank you for your kind and clear explanation.
> You are right. For the three isolated and solvated systems generated using
> "solvateoct TIP3PBOX 11" we have:
> Box (x=y=z) triangulated 3-points waters sum of charges
> H-G 64,477 6598 -0.99950000
> H 51,248 3254 -0.16460000

This is concerning. Why is the charge of your system 0.16 electrons?
You should try to find the underlying cause here and fix it.

> G 37,612 1321 -0.03280000

Same here.

> My problem is how can I run the simulations with the water counts exactly
> matched between the bound and unbound simulations?
> In AMBER tutorial 21 the following values are used for
> solvatebox structure TIP3PBOX 16.50 iso
> solvatebox guest TIP3PBOX 13.16 iso
> solvatebox host TIP3PBOX 10.18 iso
> solvatebox b2host TIP3PBOX 9.91 iso
> and manually they removed waters over 1500.
> In my case I do'nt know how to choose the appropriated number of waters or
> the numbers of the
> TIP3PBOX Nr? iso
> Could you please help me?

This is not a common approach to computing interaction energies, and
probably won't work. Usually people use an approach like MM/GBSA or
MM/PBSA to do it. Interaction energies are usually computed from
simulations of a *single* host-guest system, and postprocessing the
trajectory. MM/GBSA and MM/PBSA analyses, as with LIE analyses I
mentioned previously, make use of multiple trajectories, but the solvent
is stripped out and treated implicitly.

What you should do depends on what exactly you are trying to learn, or
what precisely you are trying to compute.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 20 2015 - 08:00:03 PDT
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