normal Martini 3: Bead Interactions and Link Headers Structure Data Requirements

  • Luke Kruse
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2 months 5 days ago #9163 by Luke Kruse
Hello all,

Thank you all for your hard work in releasing Martini 3! I recently downloaded the force field parameter files for Martini 3 and have a couple questions regarding their implementation.

1. Do any beads within the same residue interact via non-bonded interactions? A note in the tryptophan residue (within aminoacids.ff) seems to suggest that this is not the case, yet an exclusions entry was not found for amino acid residues like lysine wherein the backbone bead and second side chain bead.
2. How are the [ link ] sections handled? From my cursory understanding, they seem to be used with the martinize script to help assign groups of atoms involved in inter-residue bonded interactions (BB-BB bonding, angles, and dihedrals) as well as accounting for hydrogen bonding along the backbone.
a. Is secondary structure at the amino acid residue resolution required to assign beads?
b. Are there any nonbonded interactions added by these "link"s?
c. If my understanding of the angles/dihedrals within the [ link ] headings is correct, are the angle and dihedral parameters only dependent on the secondary structure of the central bead's residue?

Thank you for you time and best wishes!
Luke Kruse

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1 month 6 days ago #9206 by riccardo
Hi Luke,

Sorry, I missed this. So:
1) In general, yes, they do. In Martini, only beads *directly* connected do not interact via non-bonded interactions. This is set with the nrexcl=1 GROMACS directive in the [moleculetype] section. Now, in ring structures, it makes sense that beads belonging to the ring do not interact via non-bonded. In some cases - like tryptophan - the nrexcl=1 doesn't cut it because not all the beads that make up the ring are directly connected. Hence, to ensure that all beads within the ring do not interact via non-bonded interactions, some explicit [exclusions] need to be added (e.g., again, this is the case for tryptophan).
2) I'm not the martinize2 expert here, so somebody hopefully will correct me if I say some BS. [ links ] take care of the connection between different residues: that usually means adding bonds/angles/dihedrals/etc potentials between consecutive residues.
a. In Martini3, the amino acid backbone beads are now secondary-structure independent;
b. (I would say) no;
c. The dependency on the secondary structure is the only dependency of such angle/dihedral parameters that I can see. But here it would really help if somebody up-to-date with the latest martinize2 developments help clear this out.

Hope this helps

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