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] |
|
| [DSSP] |
|