[gmx-users] Error DSSP Gromacs 5.0.4

Thu Nov 5 16:26:48 CET 2015

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

—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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