Appendix to the Supplementary
Material to
All-atom empirical force field for nucleic acids: 1)
Parameter optimization based on small molecule
and condensed phase macromolecular target data.
Nicolas Foloppe1 and Alexander D. MacKerell, Jr.*
Table A1) Residue names of the model compounds in the CHARMM27 topology
file (Table A2)
Compound Topology Name/descriptor
THF, Figure 3A, interaction with water THFO, Figure 3B, interaction with water
A DMPA
B T5PH
TH5P, compound B with dianionic phosphate, vibrational analysis
C T3PH
R3PH, compound C with 2’ hydroxyl
D T3PM
E THFI, with imidazole
THMI, compound E with imidazole and 5’methyl, vibrational analysis TGUA, TADE, TCYT, TTHY, TURAa
F TM3P
RM3P, compound F, monoanionic with 2’hydroxyl
G THAO, with imidazole
NUSG, NUSA, NUSC, NUST, NUSUb RNUS, with imidazole, ribo analog
Guanine base GUA, with patch PURG or 9MG (9-methyl) or 9EG (9-ethyl) Adenine base ADE, with patch PURA or 9MA (9-methyl)
Thymine base THY, with patch PYRT or 1MT (1-methyl) Uracil base URA, with patch PYRU or 1MU (1-methyl) Cytosine base CYT, with patch PYRC or 1MC (1-methyl)
See Figure 2 for diagrams of the compounds. In certain cases it is necessary to select a residue and then modify via a patch, for example to create the guanine base the residue GUA is modified by the patch PURG.
a) Compound E with the the standard nucleic acid bases. b) Comound G with the standard nucleic acid bases.
