[gmx-users] again gmxcheck

[Grazia Daminelli]

hello everybody!

I would like to check if there is any problem in my topology file. By using
gmxcheck -f traj.trr -s1 topol.tpr
I get an incredible long list of the type:

Distance between atoms 1 and 2 is 0.101, should be 0.010
Distance between atoms 1 and 3 is 0.100, should be 0.010
Distance between atoms 1 and 4 is 0.102, should be 0.010
Distance between atoms 1 and 5 is 0.150, should be 0.022
Distance between atoms 5 and 6 is 0.153, should be 0.023
Distance between atoms 5 and 9 is 0.153, should be 0.023
....

Atoms from 1 to 10 belong to the serine residue, so that atom 1 is N, 
atoms 2,3,4 are H, atom 5 is CA.
I have problems in understanding the above output:
is there a unit problem when comparing trajectory and tpr files ?
can it be that N is called atom 1 in the trajectory file and atom 0 in 
the topol.tpr file?

if gmxcheck is working correctly, then my  topol.tpr is completely 
wrong, how  can I find out  the mistake?

thanks for any comment/explanation

Grazia