Mark Abraham Mark.Abraham at anu.edu.au
Mon Jul 27 17:04:51 CEST 2009

Morteza Khabiri wrote:
> Dear gmxusers.
> I want to restrain the lipids in my system which contains protein,lipid
> and water. I make the restraint itp file by genpr then I added it in
> toplogy file.
> After doing grompp to make tpr file I get the following message:
> Fatal error:
> [ file "posre_entirelipid1.itp", line 56 ]:
>              Atom index (53) in position_restraints out of bounds (1-52)
> I found the similar error in the mailing list and they suggested probably
> the place of restraint itp file which was included in  topology file is
> wrong.  However, I tried several positions for restraint itp but I think
> it is not the
> solution. Do you have any other suggestion about this problem??????

You're using a [ position_restraints ] directive that requires at least 
53 atoms in a position where only 52 are defined. There are various 
explanations, including #including in the wrong place, or #including a 
wrong file. Look carefully at a correct example.


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