Dear Jason,
my average structure have waters. I have checked that the waters were
centralized at a particular position.
Now I have removed the waters from my average structure and minimized it.
Many thanks to you.
----indrajit
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Fri, Jun 5, 2015 at 10:24 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Jun 5, 2015 at 12:34 PM, Indrajit Deb <biky2004indra.gmail.com>
> wrote:
>
> > Dear Jason,
> >
> > Thanks for the information. The cpptraj command worked.
> > But the problem is that, when I am using this newly prepared rst7 file as
> > an input coordinate (-c average.rst7), sander giving the following
> > error-------------
> >
> > | peek_ewald_inpcrd: Box info not found in inpcrd
> >
>
> This happens when you ask for periodic boundary conditions (ntb=1 or 2) but
> don't have an inpcrd file with box dimensions.
>
>
> > What should I do now ?
> >
>
> Does your average structure have waters? How did you get reasonable
> waters in an average structure?
>
> You can copy the last line of one of your restart files that *has* box
> information into the last line of your average.rst7 file, but I can't see
> how your waters could possibly be reasonable in an average structure.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Jun 05 2015 - 10:30:02 PDT
