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

[Tsjerk Wassenaar]

Hi Peggy,

I suspect that in your .mdp file you have a line

xtc-grps = Protein

This means that the xtc file will only contain those atoms which
gromacs reckognizes as amino acids, based on the list in the file
aminoacids.dat. Your .tpr file which is used to base the index on,
contains all atoms, including the Ca/Cl. You can easily check how many
atoms there are in your xtc file using gmxcheck and compare this to
the groups you see based on the .tpr as you've given. If you need the
calcium and chloride in the trajectory while you've only written
Protein, you'll have to redo the simulation, changing the xtc-grps
line in the .mdp, copy the file aminoacids.dat and add the ions to it
or use an index file when running grompp. Of course you can first have
a look at teh .trr file which contains all atoms by definition, but
that is usually written much less frequent.

Cheers,

Tsjerk

On Thu, Apr 10, 2008 at 8:27 AM, Peggy Yao <peggy.yao at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623