Hi,
I can confirm there is indeed a bug. It's a small 1-letter typo that
results in the reference mask always being set to the target mask. I
will start working on a bug fix. Thanks for the report.
-Dan
On Wed, Oct 5, 2016 at 9:13 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Dan,
>
> Sorry, version from amber 16 (updated with all patches on July 11) ...
>
> Well, I do not have the input and output of the failed jobs anymore as I
> now tricked the system to create a reference that includes exactly the
> same residues and it now because I don't need to use different masks
> (this is not ideal for my system but its OK, it works).. This was
> somehow urgent so I decided to fix it fast and "dirty" and all files
> were overwritten.
>
> But the error is: cpptraj does not properly read the <refmask> given to
> the drmsd command (as a second mask right after the first mask). The
> same command line but with "rmsd" instead of "drmsd" works just fine
> ... I guess there should be some easy test jobs to test if this is
> reproducible in your hands. If not possible, I will come back to you
> next week with a properly documented case ...
>
> Best wishes
> Vlad
>
>
>
>
> On 10/05/2016 02:56 PM, Daniel Roe wrote:
>> Hi,
>>
>> What version of cpptraj are you using. Also, can you please post your
>> complete input and output? Thanks.
>>
>> -Dan
>>
>> On Tue, Oct 4, 2016 at 5:14 PM, Vlad Cojocaru
>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>> Dear all,
>>>
>>> I am trying to run a "drmsd" to reference analysis in cpptraj. The atoms
>>> selected in the trajectory and the reference need to be defined by 2
>>> distinct masks (mask and refmask).
>>>
>>> Therefore I used the command: "drmsd [name] [mask] [refmask] out
>>> [filename] reference".
>>>
>>> Awkwardly, the program exits with error "Setup failed for drmsd;
>>> Detected divide by 0".
>>>
>>> Looking in the output file, I noticed that it states that the mask
>>> defined for the reference is "mask" and not "refmask" as it should. The
>>> program apparently fails to read the "refmask" I provide under the drmsd
>>> command. Importantly, the "rmsd" command runs correctly in the same
>>> conditions (same syntax).
>>>
>>> Is this a bug ?
>>>
>>> Best wishes
>>> Vlad
>>>
>>>
>>> --
>>> Dr. Vlad Cojocaru
>>> Computational Structural Biology Laboratory
>>> Department of Cell and Developmental Biology
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Oct 05 2016 - 07:00:02 PDT
