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

[gromacs query]

Hi All

Am just thinking if my mail was spammed.

Thanks for any help.

On Mon, Jun 22, 2015 at 4:58 PM, gromacs query <gromacsquery at gmail.com>
wrote:

> 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
>