[gmx-users] DSSP installation
joao.m.a.henriques at gmail.com
Sat Dec 9 11:29:44 CET 2017
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
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>
> 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
> Then I tried using the version -ver 3
> But still the error comes.
> Please help me to fix this problem.
> Sunipa Sarkar
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users