Citation

When using these files please cite:

F. M. Sousa, L. M. P. Lima, C. Arnarez, M. M. Pereira, M. N. Melo Coarse-grained parameterization of nucleotide cofactors and metabolites: protonation constants, partition coefficients, and model topologies.

Journal of Chemical Information and Modeling, 2021, 10.1021/acs.jcim.0c01077

Contents

This repo contains several files stemming from/supporting the above-mentioned paper:

• Two molecule topology description files, in text format compatible with the GROMACS software (nucleotides.itp contains the Martini CG parameters for all the parameterized molecules, and gromos_extra.itp contains the united-atom GROMOS parameters used for TPP and FAD, not available in the GROMOS distribution);
• Subdirectory mappings with atomistic-to-CG mapping descriptions for automation of conversion from the PDB or from GROMOS atomistic structures, for use with the backward resolution transformation script;
• The gmx_2019.6_restricted-bending-fep.patch patch file describing a small change necessary for GROMACS free-energy perturbation code compatibility with the use of restricted bending angle potentials (as detailed in the paper's Supporting Section S3.6).

CG Mapping

Mapping files in the mappings subdir are provided for use with the backward script. (http://www.cgmartini.nl/index.php/downloads/tools/240-backward) They contain the CG mapping of representative cofactors from structures in either the GROMOS nomenclature or the PDB nomenclature. File names indicate the Martini cofactor acronym, but their [ molecule ] directive indicates the name in the respective nomenclature. PDB names and atom nomenclatures were taken from http://ligand-expo.rcsb.org/index.html

The backward script only accepts atomistic nomenclatures from a small hardcoded list. Because the PBC nomenclature is absent from that list, the PDB mapping files refer to their atomistic topology as 'charmm'.

To CG-map a cofactor:

• Unpack the backward files;
• Place these .map files in the backward-v5/Mapping directory;
• For a structure 'cofactor.pdb' in the PDB nomenclature run:

backward-v5/backward.py -f cofactor.pdb -o cofactor.gro -from charmm -to martini

• For a structure 'cofactor.pdb' in the GROMOS nomenclature run:

backward-v5/backward.py -f cofactor.pdb -o cofactor.gro -from gromos -to martini

Limitations:

When mapping from GROMOS, the backward script cannot guess the mass of some atoms whose names do not start by their element's letter. In that case CG, bead positions may be mapped off-center. A short energy minimization will bring these beads to their equilibrium interparticle distances.

If the precise mapped position is needed from a GROMOS source, an alternative approach can be used, as was done in the paper above:

• A GROMACS index file should be constructed from the mapping, with one group per CG bead, discriminating each atom mapped to that bead. As an example for ATP:

#file 'ATP.map.ndx'
[ ADN1 ]
5 6 7 8 9 10
[ ADN2 ]
2 3 4
[ ADN3 ]
1 11 12
[ RBS1 ]
13 14 15 22
[ RBS2 ]
16 17 18 19 20 21
[ PO4A ]
23 24 25 26 27
[ PO4B ]
27 28 29 30 31
[ PO4C ]
31 32 33 34 35

• The GROMACS tool gmx traj can then be used to convert a 'cofactor.pdb' structure to a correctly-centered CG configuration. (A compatible GROMACS run input file 'cofactor.tpr' will be needed):

gmx traj -f cofactor.pdb -s cofactor.tpr -n ATP.map.ndx -com -ng 8 -oxt ATP.cg.gro

where -ng 8 is the number of groups in the .ndx file. Beware that while the resulting .gro file wll have the correct mapped positions, its bead names will be wrong.