Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations to Accurately Model Glycosaminoglycan Electrostatic Interactions
Authors/Creators
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1.
Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
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2.
Central European Institute of Technology – Masaryk University
Description
To cite and for more details: Riopedre-Fernandez et al. J. Chem. Inf. Model. 2024, 64 (18), 7122–7134. DOI: https://doi.org/10.1021/acs.jcim.4c00981
The dataset includes molecular dynamics simulations of sulfated saccharides and their sulfated analogs in the presence of calcium cations in aqueous solution. Several force field parameter sets were compared (CHARMM36, GLYCAM06, AMOEBA, Drude) and new have been developed (prosECCo75 and GLYCAM-ECC75).
The uploaded files contain the following simulation input files or/and simulation trajectories:
1) Sulfated_Molecules_Umbrella_Sampling_AIMD: Umbrella sampling ab initio molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water.
2) Sulfated_Molecules_Umbrella_Sampling_FFMD: Umbrella sampling force field molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water.
3) Sulfated_Molecules_AWH_FFMD: Accelerated weight histogram force field molecular dynamics simulations of calcium interacting with both methylsufate and N-methylsulfamate in water.
4) Disaccharides_FFMD: Unbiased force field molecular dynamics simulations of calcium-sulfated disaccharide aqueous solutions.
UPD. Version 2.0 has updated one of the disaccharide-containing simulations (GLYCAM06, N-sulfation) due to incorrect calcium LJ parameters in the original upload.