[gmx-users] DSSP installation

[João Henriques]

I already told you, use a DSSP executable that is compatible (versions 1 or
2) and pass the right version number to the -ver flag of do_dssp.

J

On Sat, Dec 9, 2017 at 1:06 PM, <spss4 at iacs.res.in> wrote:

>  ----- Message from João Henriques <joao.m.a.henriques at gmail.com>
> ---------
>     Date: Sat, 9 Dec 2017 11:29:41 +0100
>     From: João Henriques <joao.m.a.henriques at gmail.com>
> Reply-To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] DSSP installation
>       To: gmx-users at gromacs.org
>
> The output is telling you what is wrong. Gromacs doesn't support version
>> 3.
>> Install either version 1 or 2. In fact, I didn't even know there was a
>> version 3 of DSSP, where did you get it? It certainly isn't on the
>> official
>> website (http://swift.cmbi.ru.nl/gv/dssp/).
>>
>> J
>>
>> When I try version 2 there is no warning but only this fatal error comes
>>
>
>
> Program:     gmx do_dssp, version 2016.3
>  Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>
>  Fatal error:
>  Failed to execute command: Try specifying your dssp version with the -ver
>  option.
>
> I have have exported the path in bashrc file though this error comes.
> Please give any suggestion.
>
> Sunipa
>
>
>
>>
>> On Fri, Dec 8, 2017 at 4:04 PM, <spss4 at iacs.res.in> wrote:
>>
>> Hii all
>>> I want to calculate the number of helical contain of protein. For that I
>>> tried using DSSP-3.0.0(gromacs version is 2016.3). I have downloaded the
>>> tar file and extracted it. Then place the dssp fiolder in /usr/local/bin
>>> and exported the path to ./bashrc file
>>> export DSSP=/usr/local/bin/dssp
>>>
>>> Then when I was trying to use gmx do_dssp and select protein then the
>>> following error comes
>>>
>>> WARNING: You use DSSP version 3, which is not explicitly
>>> supported by do_dssp. Assuming version 2 syntax.
>>>
>>> dssp cmd='/usr/local/bin/dssp/ -i ddTLo4Hs -o ddP6o9VL > /dev/null 2>
>>> /dev/null'
>>> trr version: GMX_trn_file (single precision)
>>> Reading frame       0 time    0.000
>>> Back Off! I just backed up ddTLo4Hs to ./#ddTLo4Hs.1#
>>>
>>> -------------------------------------------------------
>>> Program:     gmx do_dssp, version 2016.3
>>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
>>>
>>> Fatal error:
>>> Failed to execute command: Try specifying your dssp version with the
>>>
>> -ver
>
>> option
>>>
>>> Then I tried using the version -ver 3
>>> But still the error comes.
>>> Please help me to fix this problem.
>>> Thanks
>>>
>>> Sunipa Sarkar
>>>
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> ----- End message from João Henriques <joao.m.a.henriques at gmail.com> -----
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