[gmx-users] do_dssp version error

[Justin Lemkul]

On 9/12/16 11:06 AM, Samith Rathnayake wrote:
> thank you
>
> I really appreciate if anyone can tell me simple and step-by step
> solution
>

There are many things that could be wrong.  Most of the normal troubleshooting 
can be found with a simple Google search (that's why we have an archive!) but I 
will sum up:

1. Run the dssp binary (NOT do_dssp) directly on a PDB file - does it work? 
This is your biggest indicator as any number of things could be wrong (binary is 
not executable, not compatible, etc).
2. Check that your DSSP environment variable is properly set.
3. What version of DSSP did you download?  The -ver flag is used by do_dssp to 
account for differences in syntax.

-Justin

>
> thank you
>
>
> regards
>
> samith
>
>
> On Mon, Sep 12, 2016 at 7:09 PM, Sarath Chandra <
> sarathchandradantu at gmail.com> wrote:
>
>> dssp by default gets installed as mkdssp.
>>
>> Do an export DSSP=path_to_mkdssp_executable
>>
>> and it will worl
>>
>> On 12 September 2016 at 18:01, Samith Rathnayake <samithzzz1 at gmail.com>
>> wrote:
>>
>>> Dear all
>>>
>>> When i'm run the do_dssp command in the gromacs
>>>
>>> do_dssp -f ../run01/run01.trr -s ../run01/run01.tpr -sc scount.xvg -o
>>> ss.xpm -dt 10 -ver 2
>>>
>>> i got this error
>>>
>>> There are 455 residues in your selected group
>>> dssp cmd='/usr/local/bin/dssp -i dd5J9xcr -o ddPd7b8G > /dev/null 2>
>>> /dev/null'
>>> trn version: GMX_trn_file (single precision)
>>> Reading frame       0 time    0.000
>>> Back Off! I just backed up dd5J9xcr to ./#dd5J9xcr.1#
>>>
>>> -------------------------------------------------------
>>> Program do_dssp, VERSION 4.6.5
>>> Source code file: /home/samith/gromacs-4.6.5/src/tools/gmx_do_dssp.c,
>>> line:
>>> 669
>>>
>>> Fatal error:
>>> Failed to execute command: Try specifying your dssp version with the -ver
>>> option.
>>>
>>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>> thank you
>>>
>>> regards
>>> samith
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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

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