Hi,
The issue here is that you're providing dry complex, dry ligand, and
dry receptor topologies, but not a solvated complex topology (i.e. one
that matches up with your solvated trajectory). Since the number of
atoms in your dry complex does not match up with the number of atoms
in your solvated trajectory there is an error. Specify the solvated
topology with the '-sp' flag and your calculation should work.
Note that this error is made a little more cryptic by the fact that
for an ASCII trajectory there is really no simple way to tell how many
atoms it contains. This problem is not present with NetCDF
trajectories; I recommend you switch to using NetCDF trajectories if
possible. For example, if I use a NetCDF version of your trajectory
instead of the ASCII one I get this error:
...
cpptraj found! Using /home/droe/Amber/GIT/amber/bin/cpptraj
Preparing trajectories for simulation...
Error: Number of atoms in NetCDF file complex1_2shots.nc (61830) does not
match number in associated parmtop (2116)!
...
which is much more informative I think.
-Dan
On Mon, Jun 10, 2013 at 7:18 AM, Senthil Natesan <sen.natesan.yahoo.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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>> AMBER mailing list
>> AMBER.ambermd.org
>> 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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> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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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 - 09:00:02 PDT
