Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 29 19:22:01 CET 2009

Liu Shiyong wrote:

> I tried to make energy groups from the "output" (*.gro)  from pdb2gmx.
>  >
> Found 0 atoms with chain identifier B
> Group is empty
>  >
> Found 0 atoms with chain identifier A
> Group is empty
> That means no chain id  information in *.gro,  but I  have to define the 
> energy groups according to chain id .

Then either specify a .pdb file as the pdb2gmx output, or instead of using chain 
identifiers, specify the residues within each group.  For example, if chain A is 
residues 1-300, then at the make_ndx prompt, type r 1-300.



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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