[gmx-users] do_dssp strange reaction

Chalaoux, Francois-Regis Francois-Regis.Chalaoux at evotec.com
Wed May 4 15:35:56 CEST 2016

Hi everybody,

Trying to use do_dssp_mpi for my MD I got an error described below.
I gave "-ver 2" for dssp 2.0.4 but nothing changed.

This is a real pain in the neck since a week to debug this message.

Any tracks Guys ?


Linux Centos 6.7
Gromacs mpi 5.04

CMD and Error
[fchalaoux at frtow0216 Complex3]$ do_dssp_mpi -f md_0_1.xtc -s md_0_1.tpr -sc scount.xvg -o ss.xpm -dt 10 -ver 2
GROMACS:    gmx do_dssp, VERSION 5.0.4

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Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
Peter Tieleman     Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

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Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
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GROMACS:      gmx do_dssp, VERSION 5.0.4
Executable:   /site/tl/app/x86_64/discovery/academic/gromacs/5.0.4/icc-2015_mkl_openmpi-1.8.5_plumed-2.1.3-sp/bin/gmx_mpi
Library dir:  /site/tl/app/x86_64/discovery/academic/gromacs/5.0.4/icc-2015_mkl_openmpi-1.8.5_plumed-2.1.3-sp/share/gromacs/top
Command line:
  do_dssp_mpi -f md_0_1.xtc -s md_0_1.tpr -sc scount.xvg -o ss.xpm -dt 10 -ver 2

Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
Group     0 (         System) has 47921 elements
Group     1 (        Protein) has  2614 elements
Group     2 (      Protein-H) has  1301 elements
Group     3 (        C-alpha) has   163 elements
Group     4 (       Backbone) has   489 elements
Group     5 (      MainChain) has   653 elements
Group     6 (   MainChain+Cb) has   805 elements
Group     7 (    MainChain+H) has   815 elements
Group     8 (      SideChain) has  1799 elements
Group     9 (    SideChain-H) has   648 elements
Group    10 (    Prot-Masses) has  2614 elements
Group    11 (    non-Protein) has 45307 elements
Group    12 (          Other) has    22 elements
Group    13 (            JZ4) has    22 elements
Group    14 (             CL) has     6 elements
Group    15 (          Water) has 45279 elements
Group    16 (            SOL) has 45279 elements
Group    17 (      non-Water) has  2642 elements
Group    18 (            Ion) has     6 elements
Group    19 (            JZ4) has    22 elements
Group    20 (             CL) has     6 elements
Group    21 ( Water_and_ions) has 45285 elements
Select a group: 5
Selected 5: 'MainChain'
There are 163 residues in your selected group
dssp cmd='/site/tl/app/x86_64/discovery/dssp/2.0.4/bin -i ddEJhJwS -o ddllnW5z > /dev/null 2> /dev/null'
Reading frame       0 time    0.000
Back Off! I just backed up ddEJhJwS to ./#ddEJhJwS.1#

Program do_dssp_mpi, VERSION 5.0.4
Source code file: /site/tl/app/x86_64/discovery/academic/gromacs/5.0.4-src/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670

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

Halting program do_dssp_mpi

gcq#48: "You Could Make More Money As a Butcher" (F. Zappa)

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

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