[gmx-users] dssp on results of HREX simulation

Shyno Mathew sm3334 at columbia.edu
Sat Oct 3 19:56:05 CEST 2015

Dear all,

I am getting errors while using do_dssp. I am able to select the main chain
for analysis.

Following is the error I am getting:

*There are 120 residues in your selected groupdssp
cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
/dev/null'Reading frame       0 time 5000.000   Back Off! I just backed up
dd7XLZVM to
do_dssp_mpi, VERSION 4.6.7Source code file:
line: 669Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.*

Here is the location of DSSP:

As mentioned in the gromacs website/mailing list, I included the path in
the .bashrc file
I tried all the following options, but I am still getting error:

export DSSP=/vega/cheme/users/sm3334/DSSP
export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs
export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi


Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University

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