[gmx-users] Fatal error in grompp

[Saumyak Mukherjee]

Dear Justin,

Thanks for the reply.

In that case, if I want the SOL-Backbone interaction energy, how shall I
choose the energygrps? Is it possible to have such a group in the index.ndx
file?

Regards,
Saumyak



‌

On 27 November 2017 at 19:05, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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>
> jalemkul at vt.edu | (540) 231-3129
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>
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-- 
Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.