AMBER: explicit implicit solvent

From: Ji-Lai Li <>
Date: Wed, 10 Jan 2007 06:24:20 -0800

Dear all:
   I have questions how to consider the solvente effects when runing
targeted md (nonperiodic).
 Some JMB papers "A shell of explicit solvent molecules was included
in the simulation and a modified TIP3P water model." (J. Mol. Biol.
(2006) 356, 237247 ant its references).
In AMBER package, the system can be prepareed by using "solvateshell"
to solvate the protein in the WAT molecules. And then minimization,
However, in the AMBER archive,
> I prefer to use solvateshell instead of solvatebox to
> decrease the time, but I am not sure if it is really
> better and I don't know what I should do for periodic
> boundary conditions.
I don't know what time it is you want to decrease. Solvateshell creates just
a sphere of water molecules about some point. It is not very accurate, since
the polarization of waters outside the "shell" is not accounted for, and there
can be unphysical effects at the water-vacuum boundary at the edge of the
water shell.
Solvateshell cannot be used for periodic simulations; use solvateBox or
solvateOct for that purpose.
..good luck...dac

 Now, I am puzzled: how to do with the solvent effects for a targeted
md simulations?

 I plan to do follow belows, but don't know if the protocol is
acceptable (the results are accurate?). 1. Solvate the solute with a
water shell (solvateshell);
2. The minimization, dynamics, etc. employed the Generalized Born model (igb=5).
  It is similar with the hybrid explicit-implicit solvent used in
Poisson-Boltzmann calculations.

I am looking forward to getting your advice.

Ji-Lai Li
State Key Laboratory of Theoretical and Computational Chemistry
Institute of Theoretical Chemistry, Jilin University
People's Republic of China
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Received on Sun Jan 14 2007 - 06:07:08 PST
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