GROMACS GAFF topologies for 26 steroid compounds

Simulation parameters (topologies) for the General Amber Force Field (GAFF) of 26 typical steroid compounds were derived and refined against experimental membrane/water partition coefficients.

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 ($K_{POPC}$), as follows. Two sets of RESP charges were derived from Hartree-Fock calculations: either in vacuum ($Q_{vac}$), or in a continuum water model ($Q_{wat}$). Then, for each steroid, the partial charges were linearly interpolated between the two sets, to best match the $K_{POPC}$ values, i.e.,

$Q_{opt} = w_{vac} Q_{vac} + (1-w_{vac})Q_{wat}$

where $w_{vac}$ was restricted to the interval [0, 1]. For steroids, for which KPOPC could not be obtained (due to solubility problems), the parameter $w_{vac}$ was guessed from steroids with similar substitutions. All $w_{vac}$ 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

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