I think you should check your amber input files. Why is it ntb set to 1 in
heat.in ? It should always be set to zero for implicit solvent simulations
!
Debayan
On Mon, May 4, 2015 at 9:44 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
> 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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> >
>
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Received on Mon May 04 2015 - 03:00:02 PDT
