[gmx-users] DSSP installation

[João Henriques]

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



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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