[gmx-users] Error DSSP Gromacs 5.0.4

João Henriques joao.henriques.32353 at gmail.com
Thu Nov 5 16:36:27 CET 2015 

Now I'm just curious, why would compiling do_dssp with MPI and/or double
precision make work incorrectly? I understand why it is absolutely
unnecessary, I just don't see why it can mess things up.

Also, running commands as root is probably the most likely cause.

/J

On Thu, Nov 5, 2015 at 4:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/5/15 10:26 AM, Stefania Evoli wrote:
>
>> I did the following steps:
>>
>> Downloaded the executable from the dssp site (dssp-2.0.4-amd64 or
>> dssp-2.0.4-i386)
>> renamed the file to dssp
>> chmod -R u=rwx dssp
>> sudo mv dssp/usr/local/bin/
>> export DSSP=/usr/local/bin/dssp
>> Added export DSSP=/usr/local/bin/dssp into the bashrc ad sourced it
>>
>>
> The problem does not come from the dssp binary.  The do_dssp program is
> just a wrapper to call dssp; do_dssp is writing intermediate dd* files that
> somehow have the wrong permission.  Your do_dssp binary (based on the name)
> is compiled as double-precision, with MPI.  Neither is necessary.
> Recompile without MPI to make sure it wasn't simply compiled wrong.
>
> Also make sure you're not trying to invoke the command via sudo, as root,
> etc.
>
> -Justin
>
>
>
>>
>>
>> —Dr. Stefania Evoli
>> Post-Doctoral Fellow
>> King Abdullah University of Science and Technology
>> Catalysis center - Bldg. 3, 4th floor, 4231–WS18
>> Thuwal, Kingdom of Saudi Arabia
>> stefania.evoli at kaust.edu.sa
>>
>>
>>
>>
>>
>>
>> On 11/5/15, 6:16 PM, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>> on
>> behalf of João Henriques"
>> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
>> joao.henriques.32353 at gmail.com> wrote:
>>
>> ​DSSP is writing dd* files with root read/write rights only.​ How did you
>>> compile it? It's hard to solve the problem without actually sitting in
>>> front of the computer and check things myself.
>>>
>>> /J
>>>
>>> On Thu, Nov 5, 2015 at 3:55 PM, Stefania Evoli
>>> <stefania.evoli at kaust.edu.sa>
>>> wrote:
>>>
>>> I tried everything discussed in the following link but the problem
>>>> remains
>>>> the same.
>>>>
>>>> [gmx-users] Problem executing do_dssp in gromacs (Aarti rana | 13 Feb
>>>> 10:41 2015)
>>>>
>>>>
>>>> I tried also ./dssp in the folder /usr/local/bin (where the executable
>>>> is
>>>> and the same of export DSSP) and it works.
>>>>
>>>> Please someone can help me? It could be a problem of version
>>>> downloaded? I
>>>> tried with both dssp-2.0.4-linux-amd64 and dssp-2.0.4-linux-i386 but
>>>> when
>>>> I ran the command do_dssp_mpi_d -f x.xtc -s x.tpr still I had the
>>>> following error
>>>>
>>>> -------------------------------------------------------
>>>> Program do_dssp_mpi_d, VERSION 5.0.4
>>>> Source code file:
>>>> /home/evolis/gromacs-5.0.4/src/gromacs/fileio/futil.cpp,
>>>> line: 863
>>>>
>>>> Fatal error:
>>>> Permission denied for opening dd4CAvLj
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>> -------------------------------------------------------
>>>>
>>>>
>>>> Thank you,
>>>> Stefania
>>>>
>>>> —Dr. Stefania Evoli
>>>> Post-Doctoral Fellow
>>>> King Abdullah University of Science and Technology
>>>> Catalysis center - Bldg. 3, 4th floor, 4231–WS18
>>>> Thuwal, Kingdom of Saudi Arabia
>>>> stefania.evoli at kaust.edu.sa
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 11/4/15, 4:29 PM, "Stefania Evoli" <stefania.evoli at kaust.edu.sa>
>>>> wrote:
>>>>
>>>> I¹m in the directory Œtest¹ that allows me to write.
>>>>>
>>>>> evolis at kw12572:~/NMDA_Llactate$ ls -lht
>>>>> total 8.5G
>>>>> drwxrwxr-x 2 evolis evolis 4.0K Nov  4 16:13 test
>>>>>
>>>>> However, after typing the do_dssp_mpi_d command, the files that are
>>>>> created by Gromacs are empty and I get the same fatal error
>>>>>
>>>>> evolis at kw12572:~/NMDA_Llactate/test$ ls -ltr
>>>>> total 13476
>>>>> -rw-rw-r-- 1 evolis evolis 8905116 Nov  4 16:12 0-50ns.xtc
>>>>> -rw-rw-r-- 1 evolis evolis 3589080 Nov  4 16:13 md.tpr
>>>>> -rw-rw-r-- 1 evolis evolis 1298388 Nov  4 16:13 index.ndx
>>>>> -rw--w---- 1 evolis evolis       0 Nov  4 16:13 ddI8Uu7p
>>>>> -rw------- 1 evolis evolis       0 Nov  4 16:15 ddRoi6XU
>>>>> -rw------- 1 evolis evolis       0 Nov  4 16:22 ddkcilMK
>>>>>
>>>>> I tried to change umask to 0000 but it doesn¹t solve the problem. Any
>>>>> ideas?
>>>>>
>>>>>
>>>>> Thanks,
>>>>> Stefania
>>>>>
>>>>> ‹Dr. Stefania Evoli
>>>>> Post-Doctoral Fellow
>>>>> King Abdullah University of Science and Technology
>>>>> Catalysis center - Bldg. 3, 4th floor, 4231­WS18
>>>>> Thuwal, Kingdom of Saudi Arabia
>>>>> stefania.evoli at kaust.edu.sa
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 11/4/15, 4:13 PM, "
>>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>>>>>
>>>> on
>>>>
>>>>> behalf of João Henriques"
>>>>> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
>>>>> joao.henriques.32353 at gmail.com> wrote:
>>>>>
>>>>> Probably has nothing to do with dssp and/or gromacs. Sounds like you
>>>>>>
>>>>> just
>>>>
>>>>> don't have permission to read and/or operate on the file. Have you
>>>>>> checked
>>>>>> the permissions of your work directory and similar stuff?
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> /J
>>>>>> --
>>>>>> Gromacs Users mailing list
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>>>>>
>>>>>
>>>>
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>> ________________________________
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>> This message and its contents including attachments are intended solely
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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