[gmx-users] do_dssp version error

[Samith Rathnayake]

located on /usr/local/bin/dssp . thus in my .bashrc i do not set the DSSP
environment.

On Mon, Sep 12, 2016 at 9:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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>>>>>>
>>>>>> --
>>>> ==================================================
>>>>
>>>> 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
>
> ==================================================
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> Gromacs Users mailing list
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