[gmx-users] Naming convention for Acetyl Terminal group

[Mark Abraham]

Hi,

That's just arbitrary. The alpha, beta, etc nomenclature does not apply to
such a capping group, so they named the carbon using H rather than A, B,
etc. Then the names of the H atoms follows that. That probably simplifies
the job of some bits of code.

Mark

On Fri., 15 Mar. 2019, 16:28 Neena Susan Eappen, <
neena.susaneappen at mail.utoronto.ca> wrote:

> 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
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