Hi Dan,
Yes I am using the most up-to-date version. The trajectory looks fine in VMD.
I will send you the files shortly.
Thanks,
Senthil
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
To: Senthil Natesan <sen.natesan.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, June 7, 2013 10:22 AM
Subject: Re: [AMBER] MMPBSA.py Error
Hi,
Are you using the most up-to-date version of AmberTools 13? You can
check by running update_amber in your $AMBERHOME directory. Remember
that after patches are applied you need to recompile in order for them
to take effect.
Can you load the complex topology and trajectory in another program
like cpptraj or VMD? It may help to track down what may be going on if
you provide me (off-list) your topology files and a shorter version of
your trajectory (~2 frames).
-Dan
On Fri, Jun 7, 2013 at 7:06 AM, Senthil Natesan <sen.natesan.yahoo.com> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jun 10 2013 - 06:30:04 PDT
