[gmx-users] Fatal error: You selected groups with differen number of atoms.

[gromacs query]

Hi All

I want to align small residues based on 3 atom names only (ignoring rest of
the atoms) and confrms does not require same number of atoms: first.pdb
with 7 atoms and second.pdb with 3 atoms.

echo "0" "0"| gmx confrms -f1 first.pdb.pdb -f2 second.pdb -no -name -o
fit.pdb


I am getting error Fatal error: You selected groups with differen number of
atoms.

I dont get error if tried with different residues having at least 4 atoms.
I am not sure why it would expect to have four atoms as I am aligning using
three atoms only. Again here if I provide in my second.pdb an additional
one more atom (total 4 atoms instead of 3) then it works. I don't know
where I read (please let me know!) it but I think it needs at least three
atoms in each residue which already I have and it should provide the
required two vectors.

I can send two residue pdbs as well.


Thanks for any suggestions,
Jiom