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

[Peggy Yao]

Thank you for your reply, Tsjerk!

I used gmxcheck, and got exactly the same number of atoms in xtc file as
#proteinAtoms+#calciumAtoms+#chlorideAtom.

I also checked my mdp file. It does have "xtc_grps = protein Ca Cl".

In previous similar runs, I successfully wrote these atoms out. The only
difference is that, in previous runs, I added some Na+ ions too. At the end
of the .top file, I had:
Protein_A           1
Na  15
Cl 12
SOL 7254
And, in mdp file, I had: xtc_grps = protein Ca Na Cl

But this time, I didn't add any Na+ ion. After genion step, the end of the
.top file became:
Protein_A           1
SOL         7280
Na          0
Cl          1
In mdp file, I had: xtc_grps = protein Ca Cl

Will this difference cause the problem? How should I solve it? Thanks a lot!

Peggy

On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:

> 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
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