General Overview

VerMoUTH and martinize2 are tools for setting up starting structures for molecular dynamics (MD) simulations starting from atomistic coordinates, with a special focus on polymeric systems (including proteins and DNA). Existing tools that do this are generally limited to strictly linear polymers, while VerMoUTH and martinize2 make no assumptions regarding polymer structure. VerMoUTH is a python library that can be used programmatically. Martinize2 is a command line tool build on top of that.

VerMoUTH and martinize2 are also capable of dealing with structures where atom names are not provided, and to some extent with incomplete structures where atoms are missing from the input structure due to e.g. experimental limitations. There is also support for post-translational modifications.

VerMoUTH and martinize2 can be used to generate both atomistic and coarse-grained topologies and are the preferred method of generating topologies for the [Martini3] force field.

Installation instructions

Vermouth and martinize2 are distributed through pypi and can be installed using pip.

pip install vermouth

The behavior of the pip command can vary depending on the specificity of your python installation. See the documentation on installing a python package to learn more.

Vermouth has SciPy as optional dependency. If available it will be used to accelerate the distance calculations when making bonds

Quickstart

The CLI of martinize2 is very similar to that of martinize1, and can often be used as a drop-in replacement. For example:

martinize2 -f lysozyme.pdb -x cg_protein.pdb -o topol.top
    -ff martini3001 -dssp -elastic

This will read an atomistic lysozyme.pdb and produce a Martini3 compatible structure and topology at cg_protein.pdb and topol.top respectively. It will use the program [DSSP] to determine the proteins secondary structure (which influences the topology), and produce an elastic network. See martinize2 -h for more options! Note that if martinize2 runs into problems where the produced topology might be invalid it will issue warnings. If this is the case it won’t write any output files, but also see the -maxwarn flag.

General layout

In VerMoUTH a force field is defined as a collection of Blocks, Links and Modifications. Each of these is a graph, where nodes describe atoms (or coarse-grained beads) and edges describe bonds between these. Blocks describe idealized residues/monomeric repeat units and their MD parameters and interactions. Links are molecular fragments that describe MD parameters and interactions between residues/monomeric repeat units. Modifications are molecular fragments that describe deviations from Blocks, such as post-translational modifications and protonation states. Mappings describe how molecular fragments can be converted between force fields.

Finally, martinize2 is a pipeline that is built up from Processors, which are defined by VerMoUTH. Processors are isolated steps which function on either the complete system, or single molecules.

Martinize2 identifies atoms mostly based on their connectivity. We read the bonds present in the input file (as CONECT records), and besides that we guess bonds based on atom names (within residues) and on distances (between residues, using the same criteria as [VMD]). This means that your input structure must be reasonable.

Citing

A publication for vermouth and martinize 2 is currently being written. For now, please cite the relevant chapter from the thesis of Peter C Kroon:

Kroon, P.C. (2020). Martinize 2 – VerMoUTH. Aggregate, automate, assemble (pp. 16-53). ISBN: 978-94-034-2581-8.

References

Martini3

P.C.T. Souza, R. Alessandri, J. Barnoud, S. Thallmair, I. Faustino, F. Grünewald, et al., Martini 3: a general purpose force field for coarse-grained molecular dynamics, Nat. Methods. 18 (2021) 382–388. doi:10.1038/s41592-021-01098-3.

VMD
  1. Humphrey, A. Dalke and K. Schulten, “VMD - Visual Molecular Dynamics”, J. Molec. Graphics, 1996, vol. 14, pp. 33-38. http://www.ks.uiuc.edu/Research/vmd/.

DSSP
  • W.G. Touw, C. Baakman, J. Black, T.A.H. te Beek, E. Krieger, R.P. Joosten, et al., A series of PDB-related databanks for everyday needs, Nucleic Acids Res. 43 (2015) D364–D368. doi:10.1093/nar/gku1028.

    1. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features., Biopolymers. 22 (1983) 2577–637. doi:10.1002/bip.360221211.