[gmx-users] xtc files
yas102 at psu.edu
Tue Mar 14 02:25:43 CET 2006
How do I convert xtc files exported for a subset of atoms in my system to pdb
When I run trjconv, I get the following error message:
Fatal error: Index 3611 is larger than the number of atoms in the trajectory
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?
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