[gmx-users] Fatal error in grompp

[Justin Lemkul]

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

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

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