[gmx-users] Error DSSP Gromacs 5.0.4

[João Henriques]

​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
> >>--
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