Re: [AMBER] Implicit water for MD studies

From: Carlos Simmerling <>
Date: Fri, 1 May 2015 12:13:38 -0400

Igb=8 was trained on biomolecules , so for a small organic you may want to
use igb=1. Most of the gb models give similar results on small molecules
anyway, the changes tend to be about how to handle buried atoms.
On Fri, May 1, 2015 at 9:17 AM, Shreeramesh <> wrote:

> Dear All,
> I want to do MD for a single oranic molecule using IMPLICIT water. In
> tleap, I have not buit solvated box and I got the following error
> Error: Box parameters not found in inpcrd file!

​This occurs because you are asking for a periodic boundary simulation in
your sander input file.

> Can you please help me to do MD using implicit water?

​Fix your input file to use a GB model. Part of the first tutorial walks
through how to run a simulation in implicit solvent. See here:

​Note there are better GB models to use than igb=1 (in particular, igb=8 is
a much better model), but the tutorial does show the general process of
setting up an implicit solvent calculation.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
AMBER mailing list
Received on Fri May 01 2015 - 09:30:04 PDT
Custom Search