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
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Received on Wed Oct 05 2016 - 06:30:04 PDT
