On the mapping of the adenosine molecule

[yuqingxiong96]

Hi, I want to use the Martini3 model to find the binding pocket of the protein. And the molecule is similar with the adenosine. So I am trying to map the adenosine. I read the itp fire for the adenosine from models/martini_v3.0.0_small_molecules_2020PCTSouzaNatCommun.itp and the Supplementary Information for "Protein-ligand binding with the coarse-grained Martini model". I want to know if TN3a and TN5a refer to the two N and one C on the adenine? I know TC6 as the virtual site because that tow rings be modeled with a "hinge" construction, but I'm confused about the TN5a as the virtual site. And the mass of tiny and small beads is 36.79 and 60.05, how to calculate it?

[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: https://github.com/ricalessandri/Martini3-small-molecules/blob/2113a594c2b52ce56dfc957d520d7718957b6107/collections/martini_v3.0.0_small_molecules_2020PCTSouzaNatCommun.itp#L250-L270

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.