Re: [AMBER] how to convert pdb to rst file ?

From: Jason Swails <>
Date: Fri, 5 Jun 2015 12:54:24 -0400

On Fri, Jun 5, 2015 at 12:34 PM, Indrajit Deb <>

> 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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jun 05 2015 - 10:00:03 PDT
Custom Search