Gmx chi Alanine residues output

User discussions
1

GROMACS version: 2024
GROMACS modification: No

Hi everyone!

I’d like to create the dihedral-time function of a protein’s amino acid sidechains. However, the gmx command doesn’t generate the values for Alanine residues’ chi dihedrals.

I used these arguments:

-all -rad -maxchi 1 -HChi

I have found the entries of the alanine chi1 dihedrals in the topology generated by CHARMM-GUI. Is it possible to somehow make a time function of a trajectory for Ala chi dihedrals?

2

To have a chi1 side chain torsional angle, by definition, you need Cbeta and Cgamma atoms, which Ala does not have