[gmx-users] trjconv not able to generated output

[Sergio Manzetti]

Hi, I have tried several ways to get the last frame from the output xtc using gmx trjconv, like: 

sem at Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 
:-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: 

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Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch 
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen 
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner 
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 Teemu Virolainen Christian Wennberg Maarten Wolf 
and the project leaders: 
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel 

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GROMACS: gmx trjconv, VERSION 5.1.2 
Executable: /usr/bin/gmx 
Data prefix: /usr 
Command line: 
gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 

Will write gro: Coordinate file in Gromos-87 format 
Reading file topol.tpr, VERSION 5.1.2 (single precision) 
Reading file topol.tpr, VERSION 5.1.2 (single precision) 
Select group for output 
Group 0 ( System) has 50510 elements 
Group 1 ( DNA) has 1333 elements 
Group 2 ( NA) has 71 elements 
Group 3 ( CL) has 31 elements 
Group 4 ( PRB) has 28 elements 
Group 5 ( Ion) has 102 elements 
Group 6 ( NA) has 71 elements 
Group 7 ( CL) has 31 elements 
Group 8 ( PRB) has 28 elements 
Group 9 ( Other) has 28 elements 
Group 10 ( NA) has 71 elements 
Group 11 ( CL) has 31 elements 
Group 12 ( PRB) has 28 elements 
Group 13 ( Water) has 49047 elements 
Group 14 ( SOL) has 49047 elements 
Group 15 ( non-Water) has 1463 elements 
Group 16 ( Water_and_ions) has 49149 elements 
Select a group: 15 
Selected 15: 'non-Water' 
Reading frame 0 time 2000.000 
Precision of traj_c.xtc is 0.001 (nm) 
Using output precision of 0.001 (nm) 

Back Off! I just backed up confout.gro to ./#confout.gro.1# 
Last frame 0 time 2000.000 

however, something is wrong with the trajectory, even tried the xtc, same problem there. There seems to be enough frames, but they don't "appear" after the selection of groups. 

How can I repair or check a trajectory? 

Sergio Manzetti 

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