[gmx-users] Fatal error: Atomtype O2 not found

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 9 14:07:55 CEST 2012

On 6/9/12 7:24 AM, ramaraju801 wrote:
> hi
> am working on a DNA-protein complex, during the energy minimization step its
> giving the following error,
> "Fatal error:
> Atomtype O2 not found"
> am using charmm27 force field and used the command "grompp -f minim.mdp -c
> protein.gro -p protein.top -o protein-EM-vacuum.tpr "

How did you produce the topology?  Did you modify it in any way?  As the error 
message states, O2 is not a valid atom type for CHARMM27.



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


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