[gmx-users] GMX Helix Segmentation fault

[David van der Spoel]

Den 2018-10-16 kl. 11:14, skrev Budheswar Dehury:
> Dear All,
> 
> 
> Hello. I am doing analysis soem analysis of TM helix properties using the GMX helix tool of GROMACS 2018.2. Though, in someways its working in the old version 2016.2 but its not working in the latest 2018.2 version. I have appended the following error.
If this is reproducible please make a small test system and upload a bug 
report at https://redmine.gromacs.org
> 
> 
> gmx helix -f ../md.xtc -s ../md.tpr -n index.ndx
> 
> Reading file ../md.tpr, VERSION 2018.2 (single precision)
> Reading frame       0 time 200000.000   Please select a group containing the entire backbone
> Group     0 (         System) has 201382 elements
> Group     1 (        Protein) has 22327 elements
> Group     2 (      Protein-H) has 11159 elements
> Group     3 (        C-alpha) has  1414 elements
> Group     4 (       Backbone) has  4242 elements
> Group     5 (      MainChain) has  5651 elements
> Group     6 (   MainChain+Cb) has  6978 elements
> Group     7 (    MainChain+H) has  6986 elements
> Group     8 (      SideChain) has 15341 elements
> Group     9 (    SideChain-H) has  5508 elements
> Group    10 (    Prot-Masses) has 22327 elements
> Group    11 (    non-Protein) has 179055 elements
> Group    12 (          Other) has 179055 elements
> Group    13 (           POPC) has 40468 elements
> Group    14 (           TIP3) has 138315 elements
> Group    15 (            SOD) has   146 elements
> Group    16 (            CLA) has   126 elements
> Group    17 (  a_10743-11091) has   349 elements
> Select a group: 17
> Selected 17: 'a_10743-11091'
> Checking group a_10743-11091
> There are 21 residues
> There are 19 complete backbone residues (from 2 to 20)
> nall=349
> Reading file ../md.tpr, VERSION 2018.2 (single precision)
> 
> Please help me to rectify this error or suggest any idea how should I get reed of this.
> 
> Thanking you
> With Warm Regards
> Budheswar
> 
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se