Re: [AMBER] Generating an average structure from a rst/pdb list?

From: Daniel Roe <>
Date: Thu, 3 Mar 2011 13:54:31 -0500


On Thu, Mar 3, 2011 at 12:21 PM, Baptiste Legrand <> wrote:
> I have first tried to trajin all my rst but it seems that only the first
> file is taken in account:

How do you know only the first file is taken into account (are there
error messages etc)?

> So in a second stage, I have concatenated with the cat command and then
> launch the my traj script:

You can't concatentate restart files - by design they contain only one
set of coordinates (and optionally velocities). Only the first set
will be read.

>   Checking coordinates: all.rst
> readAmberRestart(): topology/coordinates file are inconsist with
> NATOMS = 1138 (1248)

This indicates that the number of atoms in your topology does not
match the number of atoms in the restart file, I suspect as a result
of the 'STRIP :CL3'. You would need to generate a new topology file
without :CL3 in order to process files stripped of :CL3.


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Received on Thu Mar 03 2011 - 11:00:06 PST
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