[gmx-users] position restraints

[Outi Maija Salo]

Hi!

I was about to do a position restrained mdrun and grompp said:

Fatal error: [ file "backbone_B_fix.itp", line 3 ]:
             Atom index (3712) in position_restraints out of bounds (1-1431)


I have one protein but in three parts (A/B/C) as there are some residues
missing in between. topol_A/B/C.itp files each have atom numbers starting
from
number one even though in gro file the atom numbers are continuous from
one up to 5000 something. Could this explain the problem? How can I change
the numbers in itp files to be continuous with regard to each other? Or is
there another way to solve the problem?

Thanks!

Outi Salo
University of Kuopio
Finland