On the mapping of the adenosine molecule about martini3-small-molecules

[ricalessandri]

Hi @yuqingxiong96 . So, adenosine is mapped according to this scheme (I think this makes clear which atom belongs to which bead): https://github.com/ricalessandri/Martini3-mappings/blob/main/adenosine.pdf

And here's the topology:

Martini3-small-molecules/collections/martini_v3.0.0_small_molecules_2020PCTSouzaNatCommun.itp

Lines 250 to 270 in 2113a59

	;;;;;; ADENOSINE
	;
	; Reference(s):
	; PCT Souza, S Thallmair, P Conflitti, JC Ramirez Palacios, R Alessandri, S Raniolo, V Limongelli, SJ Marrink, Protein-Ligand
	; Binding with the Coarse-Grained Martini Model, Nat. Commun. 2020, 11, 3714, [DOI: 10.1038/s41467-020-17437-5].
	;
	[ moleculetype ]
	; Name nrexcl
	ADEN 1
	[ atoms ]
	; nr type resnr residue atom cgnr charge mass
	1 TN1 1 ADEN N1 1 0 36.79
	2 TN3a 1 ADEN N2 2 0 36.79
	3 TN5a 1 ADEN N3 3 0 0.0
	4 TP1d 1 ADEN N4 4 0 36.79
	5 TN3a 1 ADEN N5 5 0 36.79
	6 TC6 1 ADEN C6 6 0 0.0
	7 SP2 1 ADEN O7 7 0 60.05
	8 SP3 1 ADEN O8 8 0 60.05

To your questions:

• TN5a and TN3a mapping. TN5a maps the C=N group; TN3a maps only the N (so, this molecule is a little "overmapped" if you consider only the aromatic ring).
• TN5a bead as a virtual site. This allows us to reduce the number of constrains in this model.
• Masses. In this case, we used the actual mass of adenosine (~267 g/mol) and each bead on the sugar is assigned the mass that it describes (for example, bead SP2 is O-CH-CH2-OH, which means mass 16+12+1+12+2+16+1=60, and similarly for SP3) while the mass of the ring is equally shared among all the non-virtual beads.

Let me know if this clears out the doubts or not.