Molecular dynamics simulation trajectories of binding of N-acetylglucosamine
mono- ((GlcNAc)1), di- ((GlcNAc)2) and trisaccharide ((GlcNAc)3) onto hevein
domain HEV32. Systems containing one molecule of HEV32, one molecule of
an oligosaccharide and 2271-2287 water molecules were simulated for
2 microseconds. Two replicates were done for each system. Binding of
oligosaccharides into their experimentally verified binding sites was observed
in three of six simulations. Gromacs trajectories do not contain water
molecules and are are sampled every 100 ps. Gromacs structures (*.gro) and
trajectories (*.xtc) can be opened in Gromacs (analysis), Visual Molecular
Dynamics (visualization) or other software or libraries (e.g. Plumed, MDtraj).

mono1/after_mdp3nw.gro
The initial structure of the first replica of the simulation of HEV32 with
(GlcNAc)1.

mono1/md.xtc
The trajectory of the first replica of the simulation of HEV32 with (GlcNAc)1.

mono2/after_mdp3nw.gro
The initial structure of the second replica of the simulation of HEV32 with
(GlcNAc)1.

mono2/md.xtc
The trajectory of the second replica of the simulation of HEV32 with (GlcNAc)1.

di1/after_mdp3nw.gro
The initial structure of the first replica of the simulation of HEV32 with
(GlcNAc)2.

di1/md.xtc
The trajectory of the first replica of the simulation of HEV32 with (GlcNAc)2.

di2/after_mdp3nw.gro
The initial structure of the second replica of the simulation of HEV32 with
(GlcNAc)2.

di2/md.xtc
The trajectory of the second replica of the simulation of HEV32 with (GlcNAc)2.

tri1/after_mdp3nw.gro
The initial structure of the first replica of the simulation of HEV32 with
(GlcNAc)3.

tri1/md.xtc
The trajectory of the first replica of the simulation of HEV32 with (GlcNAc)3.

tri2/after_mdp3nw.gro
The initial structure of the second replica of the simulation of HEV32 with
(GlcNAc)3.

tri2/md.xtc
The trajectory of the second replica of the simulation of HEV32 with (GlcNAc)3.

md5sum.log
MD5 sums of files.