[gmx-users] segmentation fault gmx do_dssp

[Justin Lemkul]

On 4/10/20 5:48 PM, Sadaf Rani wrote:
> Dear Gromacs users
> I am doing an analysis of protein-ligand MD simulation of 150ns. I am
> trying to calculate secondary structure as below:-
> gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1
>
> But I am getting segmentation fault error.
>
> Reading file md.tpr, VERSION 2020-UNCHECKED (single precision)
> Reading file md.tpr, VERSION 2020-UNCHECKED (single precision)
> Not all residues were recognized (489 from 40652), the result may be
> inaccurate!
> Group     0 (         System) has 128526 elements
> Group     1 (        Protein) has  7893 elements
> Group     2 (      Protein-H) has  3971 elements
> Group     3 (        C-alpha) has   489 elements
> Group     4 (       Backbone) has  1467 elements
> Group     5 (      MainChain) has  1957 elements
> Group     6 (   MainChain+Cb) has  2415 elements
> Group     7 (    MainChain+H) has  2424 elements
> Group     8 (      SideChain) has  5469 elements
> Group     9 (    SideChain-H) has  2014 elements
> Group    10 (    Prot-Masses) has  7893 elements
> Group    11 (    non-Protein) has 120633 elements
> Group    12 (          Other) has   173 elements
> Group    13 (            G6P) has    27 elements
> Group    14 (            NAP) has    73 elements
> Group    15 (            NAS) has    73 elements
> Group    16 (             NA) has    10 elements
> Group    17 (          Water) has 120450 elements
> Group    18 (            SOL) has 120450 elements
> Group    19 (      non-Water) has  8076 elements
> Group    20 (            Ion) has    10 elements
> Group    21 (            G6P) has    27 elements
> Group    22 (            NAP) has    73 elements
> Group    23 (            NAS) has    73 elements
> Group    24 (             NA) has    10 elements
> Group    25 ( Water_and_ions) has 120460 elements
> Select a group: 5
> Selected 5: 'MainChain'
> There are 489 residues in your selected group
> dssp cmd='/usr/local/bin/dssp -i ddvbUtB6 2>/dev/null'
> Reading frame       0 time    0.000
> Back Off! I just backed up ddvbUtB6 to ./#ddvbUtB6.1#
> Segmentation fault (core dumped)
> How should I fix it. As my system is protein-ligand should I choose a group
> having protein and ligand together for this analysis?

The selection does not depend on the contents of the system; either 
MainChain or MainChain+H should work.

You need to verify that your dssp binary works correctly and that its 
version matches what is expected by GROMACS. You may need to use the 
-ver option. See the many posts on this very topic in the archive.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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