[gmx-users] Problems with restrains

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Tue Dec 4 18:33:12 CET 2001

Hi everybody.
I am trying to perform a restrained molecular dynamics simulation and I have
a problem when I try to restrain *simultaneously* the position of three
water molecules and three protein atoms.
I have included the itp files for the protein chains whith their respective
restrained position files.
In the mdp file I have defined "define = -DPOSRES_WATER" and I have also
included in the topolgy file the "#ifdef POSRES_WATER" option, restraining
the oxygen position of three water molecules.
When running the grompp program I have obtained the following message.

Fatal error: [ file "1bkv.top", line 32 ]:
             Atom index (13929) in position_restraints out of bounds (1-1)

What can I do to restrain simultaneoulsy the position of some water
molecules and some protein atoms?
Thanks in advance.

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