On 11/27/17 3:12 PM, Saumyak Mukherjee wrote:
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?
You have to have fully intact charge groups, which means including H
atoms and whatever else the force field characterizes as a full charge
group. You might be able to define such a group, but the quantity that
comes out of the calculation probably doesn't have any physical meaning.
-Justin
Regards,
Saumyak
On 27 November 2017 at 19:05, Justin Lemkul <jalem...@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
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Virginia Tech Department of Biochemistry
303 Engel Hall
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Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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