Re: [AMBER] MMPBSA.py Error

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Fri, 7 Jun 2013 06:06:04 -0700 (PDT)

Hi Jason,

Thanks for the suggestions. I looked at the trajectories and they seem fine. Nothing strange !
I tried the same trajectories and inputfiles with AmberTools1.4 &Amber11 (earlier I tried the latest versions)
along with solvated complex prmtop file and it works perfectly fine (without any error) and I got the results after 8-9 hours on a single node.

Good day !

Senthil




________________________________
 From: Jason Swails <jason.swails.gmail.com>
To: Senthil Natesan <sen.natesan.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, June 6, 2013 11:56 AM
Subject: Re: [AMBER] MMPBSA.py Error
 

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 Fri Jun 07 2013 - 06:30:02 PDT
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