I want to calculate angle between C=O of a protein residue and Cl atom of my ligand. I tried to make index file by mentioning following groups:
ri 4 & a C O | ri 130 & a F1
but the output is only 1 atom. How can i select 3 atoms simultaneously becuase gmx angle requires a triplet for angle calculation.
Jamoliddin Razzokov
You can manually insert those atom numbers to the index file.
[atoms]
4 5 130
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Madhusudan Dutta
instead of "ri" use "a" as follows
ax|ay|az where x, y and z are representing the number id of atoms of C, O and Cl.
one more thing after prepare the ndx file you should see the atoms are in correct order or not for example if you need the angle
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