[gmx-users] Naming convention for Acetyl Terminal group

[Neena Susan Eappen]

Hello gromacs users,

A small question, why is that atoms of a methyl group named/ labelled differently in an Acetyl terminal group vs Alanine (below parameters from .rtp file from OPLS-AA ff)? I do understand naming convention in the methyl group of Alanine, but not in acetyl group.

[ ACE ]
 [ atoms ]
   CH3    opls_135   -0.180     1
  HH31    opls_140    0.060     1
  HH32    opls_140    0.060     1
  HH33    opls_140    0.060     1
     C    opls_235    0.500     2
     O    opls_236   -0.500     2

AND

[ ALA ]
 [ atoms ]
     N    opls_238   -0.500     1
     H    opls_241    0.300     1
    CA    opls_224B   0.140     1
    HA    opls_140    0.060     1
    CB    opls_135   -0.180     2
   HB1    opls_140    0.060     2
   HB2    opls_140    0.060     2
   HB3    opls_140    0.060     2
     C    opls_235    0.500     3
     O    opls_236   -0.500     3

Thank you for your knowledge,
Neena