When attempting to run the RMSD analysis the program returns the following error.
Fatal error:
Masses were requested, but for some atom(s) masses could not be found in the
database. Use a tpr file as input, if possible, or add these atoms to the mass
database.
This error occurs due to the presence of two dummy atoms in my topology, which were previously detected. The command used to perform the RMSD calculation is:
gmx rms -s replica_1/first_frame.pdb -f replica_1/f5000.trajectory.xtc -o rmsd.firstframe.protein.xvg -n .rmsd.ndx
Since first_frame.pdb has no mass information, the program fails.
Would it be possible to perform RMSD analysis considering only the backbone or the alpha carbon, in order to avoid errors caused by the presence of dummy atoms?
When attempting to run the RMSD analysis the program returns the following error.
Fatal error:
Masses were requested, but for some atom(s) masses could not be found in the
database. Use a tpr file as input, if possible, or add these atoms to the mass
database.
This error occurs due to the presence of two dummy atoms in my topology, which were previously detected. The command used to perform the RMSD calculation is:
gmx rms -s replica_1/first_frame.pdb -f replica_1/f5000.trajectory.xtc -o rmsd.firstframe.protein.xvg -n .rmsd.ndx
Since first_frame.pdb has no mass information, the program fails.
Would it be possible to perform RMSD analysis considering only the backbone or the alpha carbon, in order to avoid errors caused by the presence of dummy atoms?