[gmx-users] again gmxcheck
Grazia Daminelli
Grazia.Daminelli-Widany at TU-Berlin.DE
Mon Feb 20 11:12:34 CET 2006
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
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