[gmx-users] Error DSSP Gromacs 5.0.4

Stefania Evoli stefania.evoli at kaust.edu.sa
Wed Nov 4 14:29:25 CET 2015

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


‹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?
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