[gmx-users] gmx complains of mismatch between index and trajectory file

[Mark Abraham]

Hi,

Your xtc file has only the group you wrote, so it isn't valid to index into
it with an index file that was made for a conformation with many other
atoms. That's the mismatch the message mentions. For your xtc, "System" is
the subset of *it* that you seem to want for your analysis. Note that gmx
convert-tpr -f topol.tpr -n -o subset.tpr is sometimes needed for giving an
analysis tool a matching coordinate and trajectory file. That would let you
then build eg a Protein group that was valid to index into your trajectory.

Mark

On Fri, 28 Jul 2017 01:46 Jared Sagendorf <sagendor at usc.edu> wrote:

> Hello, I'm using GROMACS 5.1.13 and ran into a problem I've never
> encountered before. I've run a simulation on a zinc-finger DNA complex and
> defined a group in my index filed called "Protein_DNA" from the default
> "Protein" and "DNA" groups. This group should contain 4666 atoms, which it
> does.
>
> $gmx make_ndx -n index.ndx
>     0 System              : 180141 atoms
>     1 Protein             :  2830 atoms <==================
>     2 Protein-H           :  1427 atoms
>     3 C-alpha             :   171 atoms
>     4 Backbone            :   513 atoms
>     5 MainChain           :   685 atoms
>     6 MainChain+Cb        :   851 atoms
>     7 MainChain+H         :   854 atoms
>     8 SideChain           :  1976 atoms
>     9 SideChain-H         :   742 atoms
>     10 Prot-Masses         :  2830 atoms
>     11 non-Protein         : 177311 atoms
>     12 Ion                 :    32 atoms
>     13 ZN                  :     7 atoms
>     14 NA                  :    25 atoms
>     15 DNA                 :  1836 atoms <=================
>     16 ZN                  :     7 atoms
>     17 NA                  :    25 atoms
>     18 Water               : 175443 atoms
>     19 SOL                 : 175443 atoms
>     20 non-Water           :  4698 atoms
>     21 Water_and_ions      : 175475 atoms
>     22 Protein_DNA         :  4666 atoms <=================
>
> I'm not sure why the ZN and NA groups show up twice, but I assume it's not
> an issue. Anyway, Protein_DNA is defined, and when I compare the values in
> the index.ndx file to the atom numbers in the .gro file, it all matches up.
>
> In my .mdp input file, I specify this group to be output as a compressed
> .xtc trajectory.
>
>     ; OUTPUT CONTROL OPTIONS =
>     nstxout                  = 10000
>     nstvout                  = 10000
>     nstfout                  = 0
>     nstlog                   = 10000
>     nstenergy                = 2500
>     nstxout-compressed       = 1000
>     compressed-x-precision   = 1000
>     compressed-x-grps        = Protein_DNA
>
> And then I run my simulation. I now have my traj.xtc file, which I want to
> process. However, when using gmx trjconv, and select the group Protein_DNA,
> I get the following error:
> $gmx trjconv -f traj.xtc -n index.ndx [options]
>     Fatal error:
>     Index[4659] 4667 is larger than the number of atoms in the
>     trajectory file (4666). There is a mismatch in the contents
>     of your -f, -s and/or -n files.
>
> The group DNA_Protein should contain 4666 atoms, and I've verified that my
> traj.xtc file indeed contains 4666 items with gmx check:
>
> $gmx check -f traj.xtc
>     Checking file traj.xtc
>     Reading frame       0 time    0.000
>     # Atoms  4666
>     ...
>
> So what is the problem here? The error message states that "Index[4659]
> 4667 is larger than the number of atoms in the trajectory file (4666)",
> which is true - the 4659th atom listed in the "Protein_DNA" index is indeed
> atom 4667, but so what? There's 4666 atoms in the index, and 4666 atoms in
> traj.xtc file - I don't see where the mismatch is.
>
> Can someone help me out with this and suggest some things to try, or
> explain what is wrong if I'm missing something?
>
> Is it possible this is related to the fact that the protein topology file
> includes 7 zinc atoms (since this is a ZF protein), which are not included
> in the group Protein_DNA? Note that if I don't supply an index file and
> choose "Protein" from the default groups, gmx
> trjconv will run, but if I choose "DNA", I get a similar error.
>
>     Fatal error:
>     Index[1829] 4667 is larger than the number of atoms in the
>     trajectory file (4666). There is a mismatch in the contents
>     of your -f, -s and/or -n files.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>