[gmx-users] Range checking error

[Mark Abraham]

namita at ncbs.res.in wrote:
> My initial input file is a model which was generated using Modeller, and
> it is a part of the original structure. I am considering fragments of a
> particular structure for my analysis. Could this be a possible problem for
> running a simulation?? I suppose there is a problem when I try to convert
> this PDB file into a .gro file. But I have no clue as to what the possible
> problem could be. The format of my input PDB file is correct.

Well, you don't need a .gro file - see 
http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file

Chopping something into fragments is a great way to make chemical 
nonsense, but pdb2gmx and grompp will often give you warnings and errors 
about such things. Read them carefully and pay attention!

> Also I tried to run a job for the original PDB structure which worked
> perfectly fine.

Well that means your problem came with something you did...

Mark