On Thu, Jun 6, 2013 at 11:46 AM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
> Dear Amber Users,
>
> I am trying to do MMPBSA calculations with a single trajectory and gives
> the following error:
>
> ----------------------------------------------
>
> Preparing trajectories for simulation...
> Error in box coord line of trajectory h3_820_complex_prod2.mdcrd.
> Expect only 3 or 6 box coords.
> Problem line: 4.509 71.808 82.630 27.602 29.349 36.456 58.340
> 102.059 -20.666
>
> Error: Could not set up h3_820_complex_prod2.mdcrd for reading.
> Error: trajin: Could not set up trajectory.
> TrajError: Trajectory h3_820_complex_prod2.mdcrd has 0 frames!
> Exiting. All files have been retained.
> --------------------------------------------------
>
> I went through the previous user lists messages, but there is no clear
> answers that I could find.
>
These error messages indicate that your trajectory file is incompatible
with the topology file it is paired with. As always with MM/PBSA-type
analyses, simple debugging starts with visualizing the problematic
trajectory (either the input trajectories or the intermediate ones with the
names like _MMPBSA_*.mdcrd.# or _MMPBSA_*.nc.#). If the files are
incompatible, it will be immediately obvious.
Note the beginning of the MMPBSA.py chapter suggests that you should be
able to run MMPBSA analyses 'by hand' to avoid treating these scripts like
a black box. When you can do this, it becomes much easier to debug issues
(or avoid them in the first place!) with MMPBSA.py
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 06 2013 - 09:00:05 PDT
