[gmx-users] problem with trjconv

[Jozef Hritz]

	Gromacs Users,

I have MD trajectory of protein dimmer. I have observed different behavior
of its monomeric units (they are structuraly identical, composed from
2065 atoms). Therefore I wanted to superimposed the second monomeric unit
to the first one and then to observe, where are the biggest structural
differences.
I have wrote [ monomer_1 ] and [ monomer_2 ] groups with corresponding 
atoms into index.ndx file and then I had run trjconv

For the initial structure:
trjconv -f first.gro -o monomer_2.gro -s run.tpr -n index.ndx -fit
rot+trans

For least squares fit I have used group [ monomer_1 ] and for output group
[ monomer_2 ]. When I have checked the output, there was no fit done. It
just took monomer_2 part from initial structure first.gro without fiting.

In the second step I wanted to fit monomer_2 part to monomer_1 during
whole MD trajectory, but as I wrote I have even problem with the first
frame.

Can anybody help me with this problem?  

Thank You
Jozef