[gmx-users] do_dssp version error

[Samith Rathnayake]

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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