Dear Sir,
Many thanks for your information and I have followed the tutorial (
http://ambermd.org/tutorials/basic/tutorial1/section4.htm) to perform MD on
small organic molecules based on implicit solvent
But, I got the following error in Heating step. It could be due to a
periodic boundary simulation in sander input file as you have pointed out.
However, I have not solvated the system using solvent box while running
tleap (The script for tleap has been attached).
*Error: Box parameters not found in inpcrd file!*
Can you please kindly help me to set up a system for small organic molecule
based on implicit solvent in tleap/MD script? I also attached all the
script including tleap for your kind attention
Thanks & regards
*Dr. Ramesh M*
Email: shreeramesh.gmail.com
Mobile: (91) + 9646469938 (27) + (0) 844556164
On Fri, May 1, 2015 at 9:13 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 Mon May 04 2015 - 02:00:03 PDT
