[gmx-users] xtc files

[YOLANDA SMALL]

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?

Thanks,
Yolanda