Re: [AMBER] Implicit water for MD studies

From: Carlos Simmerling <carlos.simmerling.gmail.com>
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 <shreeramesh.gmail.com> 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:
http://ambermd.org/tutorials/basic/tutorial1/section4.htm

​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.


HTH,
Jason

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 01 2015 - 09:30:04 PDT
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