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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 01 2015 - 07:30:02 PDT
