[gmx-users] xtc files

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 14 08:49:43 CET 2006

> Hi All,
> How do I convert xtc files exported for a subset of atoms in my system to pdb
> files?
> When I run trjconv, I get the following error message:
> Fatal error: Index[0] 3611 is larger than the number of atoms in the trajectory
> file (3152)
> In my mdp file I specify the option 'xtc_grps' to export a subset of solvent and
> protein atoms to an xtc file. This subset of atoms is defined in my index file
> and contains 3152 atoms. Then I discard the .trr files to save space.  It looks
> like the atom index gets renumbered from 1 in the new .xtc file so that the new
> atom indeces no longer correspond to the atoms in the original coordinate file.
>  How do I recover the coordinates with matching atom names from the .xtc file?
Sorry I misread your question.
You make a pdb file from your original tpr using the same index group 
you used for the xtc-grps, then you use this pdb file as reference for 
trjconv on the xtc to pdb conversion.
> Thanks,
> Yolanda
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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