Gromacs GAFF topologies for 26 steroid compounds

On this site, we provide force field topology files in GROMACS format for 26 steroid compounds.

The atom types (Lennard-Jones parameters) are standard GAFF atoms. The partial charges were optimized to reproduce partition coefficients between a POPC membrane (modelled with Slipids) and TIP3P water. The topologies were not validated against any other data, such as protein binding affinities, so use them with caution.

Methods summary: The topologies were created with AmberTools14 using GAFF atom types and RESP charges. The electrostatic potential used for the RESP fit was calculated with Gaussian using HF/6-31G* (HF/6-31+G* for the anionic compounds) level of theory. The charges were optimized to reproduce experimentally measured partition coefficients between a POPC membrane and water (KPOPC), as follows. Two sets of RESP charges were derived from Hartree-Fock calculations: either in vacuum (Qvac), or in a continuum water model (Qwat). Then, for each steroid, the partial charges were linearly interpolated between the two sets, to best match the KPOPC values, i.e.,

Qopt = wvacQvac + (1-wvac)Qwat,

where wvac was restricted to the interval [0,1]. For steroids, for which KPOPC could not be obtained (due to solubility problems), the parameter wvac was guessed from steroids with similar substitutions. All wvac values are listed in this file. The topolgies were converted to Gromacs format by ACPYPE. For more details please refer to the reference below.

These files come without any warranty of any kind, to the extent applicable by local law.

If you use these files for publication, please cite:

Rationalizing steroid interactions with lipid membranes: conformations, partitioning, and kinetics
Kalina Atkovska, Johannes Klingler, Johannes Oberwinkler, Sandro Keller, Jochen S. Hub
ACS Central Science, 4, 1155-1165 (2018) [www] [pdf] [supporting info]

Please note: We discourage the use of the cholesterol GAFF topology, since many lipid force fields provide optimized cholesterol model. The model is here only provided for the sake of completeness.

Steroid Fromula Structure file Topology file
Aldosterone ALD.pdb
ALD.itp
4-Androstenedione ASD.pdb
ASD.itp
β-Estradiol BED.pdb
BED.itp
β-Sitosterol BSL.pdb
BSL.itp
Cholesterol (discouraged) chol_gaff.pdb
chol_gaff.itp
Hydrocortisone (Cortisol) CTL.pdb
CTL.itp
Cortisone CTN.pdb
CTN.itp
Corticosterone (17-deoxycortisol) CTS.pdb
CTS.itp
Dehydroergosterol DEL.pdb
DEL.itp
Dehydroepiandrosterone DHEA.pdb
DHEA.itp
Dehydroepiandrosterone sulfate DHEAS.pdb
DHEAS.itp
Dexamethasone DMN.pdb
DMN.itp
Dihydrotestosterone DTSN.pdb
DTSN.itp
Ethinylestradiol EEL.pdb
EEL.itp
Estrone ESN.pdb
ESN.itp
Estriol ETL.pdb
ETL.itp
Fludrocortisone acetate FCA.pdb
FCA.itp
Levonorgestrel LGL.pdb
LGL.itp
Methandrostenolone MAL.pdb
MAL.itp
Pregnenolone PGN.pdb
PGN.itp
Pregnenolone acetate PGNA.pdb
PGNA.itp
Pregnenolone sulfate PGNS.pdb
PGNS.itp
Progesterone PGS.pdb
PGS.itp
Prednisone PNN.pdb
PNN.itp
Tetrahydrodeoxycorticosterone TDOC.pdb
TDOC.itp
Testosterone TSN.pdb
TSN.itp

All topologies are also available with non-optimized charges, i.e. with the original HF/6-31G* (HF/6-31+G* for the anionic compounds) RESP charges obtained in vacuum. download