[gmx-users] Bad .tpr or .xtc files?

[Peggy Yao]

Hi all,

In my system, I have 1 protein, 2 calcium atoms, and 1 chloride atom. When I
used trjconv to write the protein out as PDB file, it worked fine. However,
when I tried to write the calciums and chloride out using the same command
(but selecting different group to write out), I got the following fatal
error:

for calcium:
Select group for output
Opening library file /usr/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 22737 elements
Group     1 (     Protein) has   894 elements
Group     2 (   Protein-H) has   707 elements
Group     3 (     C-alpha) has    89 elements
Group     4 (    Backbone) has   267 elements
Group     5 (   MainChain) has   357 elements
Group     6 (MainChain+Cb) has   440 elements
Group     7 ( MainChain+H) has   447 elements
Group     8 (   SideChain) has   447 elements
Group     9 ( SideChain-H) has   350 elements
Group    10 ( Prot-Masses) has   894 elements
Group    11 ( Non-Protein) has 21843 elements
Group    12 (          Ca) has     2 elements
Group    13 (         SOL) has 21840 elements
Group    14 (          Cl) has     1 elements
Group    15 (       Other) has 21843 elements
Select a group: 12
Selected 12: 'Ca'
Reading frame       0 time    0.000
Precision of traj.xtc is 0.001 (nm)
Segmentation fault  3 time  150.000    ->  frame      3 time  150.000

for chloride:
Select group for output
Opening library file /usr/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 22737 elements
Group     1 (     Protein) has   894 elements
Group     2 (   Protein-H) has   707 elements
Group     3 (     C-alpha) has    89 elements
Group     4 (    Backbone) has   267 elements
Group     5 (   MainChain) has   357 elements
Group     6 (MainChain+Cb) has   440 elements
Group     7 ( MainChain+H) has   447 elements
Group     8 (   SideChain) has   447 elements
Group     9 ( SideChain-H) has   350 elements
Group    10 ( Prot-Masses) has   894 elements
Group    11 ( Non-Protein) has 21843 elements
Group    12 (          Ca) has     2 elements
Group    13 (         SOL) has 21840 elements
Group    14 (          Cl) has     1 elements
Group    15 (       Other) has 21843 elements
Select a group: 14
Selected 14: 'Cl'
Reading frame       0 time    0.000
Precision of traj.xtc is 0.001 (nm)
-------------------------------------------------------
Program trjconv, VERSION 3.3.2
Source code file: gmx_trjconv.c, line: 994
Fatal error:
Index[0] 22737 is larger than the number of atoms in the trajectory file
(897)
-------------------------------------------------------
Does anybody know what might be wrong? Maybe the .tpr or .xtc files are not
complete? Is there any way to check? Thanks!

Peggy
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