[gmx-users] Fatal error in grompp

Justin Lemkul jalemkul at vt.edu
Mon Nov 27 14:35:27 CET 2017

On 11/27/17 5:25 AM, Saumyak Mukherjee wrote:
> Dear All,
> I want to calculate the interaction energy between water and protein
> backbone. However, in mdp file, when I am using
> energygrps = SOL backbone
> ​grompp is returning the following error.
> Fatal error:
> atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in
> different energy groups
> Can someone kindly point out my mistake?​

You can't make the backbone a separate energy group. Look at what atoms 
1 and 2 are - likely it's the N-terminal N and one H atom, which have to 
be in the same group to do a group-based, pairwise energy decomposition. 
Whatever groups you establish have to contain full charge groups.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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