[gmx-users] error while executing do_dssp program

[Justin Lemkul]

On 12/31/14 12:18 PM, Nizar Masbukhin wrote:
> the directory where i execute the command is in desktop. i think that
> folder doesnt need write/read permission. i even have used sudo -s mode,
> still the problem exist.

Disk space, maybe?  In any case, this is a file management/permission/space 
issue, external to Gromacs.  do_dssp is simply reporting that it can't write the 
intermediate file(s) to disk in order to continue.

-Justin

> On Dec 31, 2014 11:39 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/31/14 10:53 AM, Nizar Masbukhin wrote:
>>
>>> hi gromacs user,
>>>
>>> when i try to compute secondary structure using do_dssp program, the error
>>> message appear:
>>>
>>> "Program do_dssp_mpi, VERSION 5.0.2
>>> Source code file: /home/user/gromacs-5.0.2/src/gromacs/fileio/futil.cpp,
>>> line: 863
>>>
>>> Fatal error:
>>> Permission denied for opening ddhCTh1r
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors"
>>>
>>> i have installed dssp program, and i have set the environment DSSP to the
>>> path where i install DSSP.
>>>
>>> could anyone please explain to me whats wrong?
>>>
>>>
>> You don't have write permission in the directory where you are executing
>> your command.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

==================================================