Department of Chemistry, Faculty of Science, University of Kurdistan

AMBER Parameter Database

On this page, you will find archived parameter files for the hetero groups for which we calculated parameters. The files can be downloaded for free. If you use the files in your calculations, please cite them (you can find the references in the last column of Table 1 and in the reference list at the end of this page). The parameter sets are defined in PREP (.in) and FRCMOD (.dat) files, while atom names are found in the corresponding PDB files.

To calculate GAFF parameters of hetero-molecules, they were optimized at the B3LYP/6-31G(d) [1–5] level of theory, and electrostatic potentials were calculated at the Hartree−Fock/6-31G(d) level of theory with points sampled according to the Merz−Kollman scheme [6]. They were calculated by Gaussian 16 program package [7]. Atomic charges were then fitted to these potentials using the RESP procedure [8], as implemented in the antechamber program [8], which also assigned GAFF atom types to the molecules. In the case of the connected ligands, parameters are created based on the procedure described in the AMBER-PARM page, where the Amber atom types and BCC charges are assigned.

Table 1. Parameter files for some hetero groups.

Name and description

Residue name

PREP file

FRCMOD

PDB

Ref

S-(N-hydroxy-N-bromophenyl carbamoyl) glutathione

GBP

gbp.in

gbp.dat

gbp.pdb

[9]

S-D-lactoylglutathione

SLG

slg.in

slg.dat

slg.pdb

[9]

Glutathione

GSH

gsh.in

gsh.dat

gsh.pdb

[9]

Hydroxide ion; OH⁻

XOH

xoh.in

xoh.pdb

[9]

Oxide ion; O₂⁻

O2X

o2x.in

o2x.pdb

[9]

N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide

X77

x77.in

x77.dat

x77.pdb

[10]

ZINC4092168^a

M03

m03.in

m03.dat

m03.pdb

[10]

ZINC13497421^a

M77

m77.in

m77.dat

m77.pdb

[10]

Pioglitazone, 5-(4-(2-(5-ethylpyridin-2-yl)ethoxy)benzyl)thiazolidine-2,4-dione

PIO

pio.in

pio.dat

pio.pdb

[11]

(Z)-5-((5-((3-chlorophenyl)amino)thiophen-2-yl)methylene)-3-(4-methylbenzyl) thiazolidine-2,4-dione

SPF

spf.in

spf.dat

spf.pdb

[11]

(Z)-5-((5-((2-chlorophenyl)amino)thiophen-2-yl)methylene)-3-(4-methylbenzyl) thiazolidine-2,4-dione

SPR

spr.in

spr.dat

spr.pdb

[11]

^a ZINC compound

References

[1] C. Lee, W. Yang, R.G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B. 37 (1988) 785–789. https://doi.org/10.1103/PhysRevB.37.785.

[2] A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Phys. Rev. A. 38 (1988) 3098–3100. https://doi.org/10.1103/PhysRevA.38.3098.

[3] A.D. Becke, Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys. 98 (1993) 5648–5652. https://doi.org/10.1063/1.464913.

[4] G.A. Petersson, M.A. Al‐Laham, A complete basis set model chemistry. II. Open‐shell systems and the total energies of the first‐row atoms, J. Chem. Phys. 94 (1991) 6081–6090. https://doi.org/10.1063/1.460447.

[5] G.A. Petersson, A. Bennett, T.G. Tensfeldt, M.A. Al-Laham, W.A. Shirley, J. Mantzaris, A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements, J. Chem. Phys. 89 (1988) 2193–2218. https://doi.org/10.1063/1.455064.

[6] B.H. Besler, K.M. Merz, P.A. Kollman, Atomic charges derived from semiempirical methods, J. Comput. Chem. 11 (1990) 431–439. https://doi.org/10.1002/jcc.540110404.

[7] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, G.A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V Marenich, J. Bloino, B.G. Janesko, R. Gomperts, B. Mennucci, H.P. Hratchian, J. V Ortiz, A.F. Izmaylov, J.L. Sonnenberg, Williams, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V.G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J.A. Montgomery Jr., J.E. Peralta, F. Ogliaro, M.J. Bearpark, J.J. Heyd, E.N. Brothers, K.N. Kudin, V.N. Staroverov, T.A. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A.P. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, J.M. Millam, M. Klene, C. Adamo, R. Cammi, J.W. Ochterski, R.L. Martin, K. Morokuma, O. Farkas, J.B. Foresman, D.J. Fox, Gaussian 16, (2016).

[8] C.I. Bayly, P. Cieplak, W. Cornell, P.A. Kollman, A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model, J. Phys. Chem. 97 (1993) 10269–10280. https://doi.org/10.1021/j100142a004.

[9] J. Shirazi, S. Jafari, U. Ryde, M. Irani, Catalytic Reaction Mechanism of Glyoxalase II: A Quantum Mechanics/Molecular Mechanics Study, J. Phys. Chem. B. 127 (2023) 4480–4495. https://doi.org/10.1021/acs.jpcb.3c01495.

[10] B. Sepehri, R. Ghavami, F. Mahmoudi, M. Irani, R. Ahmadi, D. Moradi, Identifying SARS-CoV-2 main protease inhibitors by applying the computer screening of a large database of molecules, SAR QSAR Environ. Res. 33 (2022) 341–356. https://doi.org/10.1080/1062936X.2022.2050424.

[11] S. Gupta, G.S. Baweja, S. Singh, M. Irani, R. Singh, V. Asati, Integrated fragment-based drug design and virtual screening techniques for exploring the antidiabetic potential of thiazolidine-2,4-diones: Design, synthesis and in vivo studies, Eur. J. Med. Chem. 261 (2023) 115826. https://doi.org/https://doi.org/10.1016/j.ejmech.2023.115826.