[gmx-users] do_dssp version error

[Samith Rathnayake]

and now this is what i got when do_dssp run : Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)

but dssp binary (NOT do_dssp) directly on a PDB file is working

On Mon, Sep 12, 2016 at 9:21 PM, Samith Rathnayake <samithzzz1 at gmail.com>
wrote:

> 1/ yes it working on pdb
> 3/dssp-2.04
>
> thank you
>
> On Mon, Sep 12, 2016 at 8:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>>>> --
>>>>> Gromacs Users mailing list
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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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>
>