[gmx-users] Ligand Virtual Sites

[Joan Clark Nicolas]

Dear GMX users,
I am trying to generate a custom virtual site for a C-NH3 group of a
ligand.
As a first test, I would like to use the parameters of the Lys virtual
site, but I can't see how the coordinates of the dummy atoms are generated
(I have already checked the tutorial and the gromacs manual). Can you help
me or redirect me to a paper/book where it is explained?

Thank you!
*Joan Clark i Nicolas*