[gmx-users] do_dssp version error

[Justin Lemkul]

On 9/12/16 11:56 AM, Samith Rathnayake wrote:
> 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
>

This is what I meant in point 2.  $DSSP needs to point to your actual dssp 
binary, wherever it is.  Either your environment variable is not set, or it is 
set incorrectly.

-Justin

> 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
>>>>>> --
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>>>>>> --
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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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>>
>>

-- 
==================================================

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

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