Re: [AMBER] question about

From: Jason Swails <>
Date: Fri, 11 Nov 2011 22:18:46 -0500

On Fri, Nov 11, 2011 at 6:42 PM, Sidney Elmer <> wrote:

> Hi,
> I am using for the first time and am getting errors:
> ---- snip ----
> Traceback (most recent call last):
> File "/raid5/amber11/bin/", line 1467, in ?
> verbose)
> File "/raid5/amber11/src/mmpbsa_py/", line 1492, in gboutput
> bonddif[x] = bonddif[x] - bond[x]
> IndexError: list index out of range
> As I was looking through the code, it appears that the program is expecting
> the number of frames in the complex mdout file to be the same as the number
> of frames in the receptor and ligand mdout files. If the number of frames
> in each of the mdout files is not the same, then one gets the IndexError
> shown above. Is this correct?

This should only be correct for a single trajectory case. For multiple
trajectories, should actually follow a different code path (for
this very reason). However, this is quite an old version of
(it's the one released with Amber 11). There's a much more recent version
released with AmberTools 1.5 that would be a better choice.

I honestly can't remember if this limitation existed (accidentally) in the
Amber 11 version of the code, but I'm pretty sure it was taken out of the
AmberTools 1.5 rewrite (and it's definitely not going to be present in the
upcoming version).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Fri Nov 11 2011 - 19:30:03 PST
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