Re: [AMBER] strange format of .rst file

From: Jason Swails <>
Date: Fri, 18 Nov 2016 12:13:43 -0500

On Fri, Nov 18, 2016 at 12:04 PM, Thakur, Abhishek <> wrote:

> Thank you
> But after converting it to ascii format I am trying to make pdb file from
> the .rst file I am getting an error

​cpptraj can convert directly to PDB -- there is no need to go to ASCII
restart first.

> Error: '*' encountered (atom 10706 Y). This indicates coordinate overflow.

​PDB files can't store arbitrarily large coordinates, since it only has 8
characters allotted to each coordinate (in angstroms). In general, PDB is
a horrible format for any kind of dynamics data. If your coordinates are
overflowing, you have two choices:

1. If your system has periodic boundary conditions, use "autoimage" in
cpptraj before writing the PDB file to wrap all of the molecules back into
the same unit cell.

2. If (1) is not an option either because there are no PBC, or your
periodic cell is comically enormous, then use a different format.


Jason M. Swails
AMBER mailing list
Received on Fri Nov 18 2016 - 09:30:03 PST
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