Molecular dynamics simulation of Conus textile conotoxin Txd13 in complex with a3b2, a3b4, a6b2 or a6b4 nAChR subtypes.

This folder contains the coordinate and parameter files used to run molecular dynamics simulations of the toxin Txd13 (sequence GCCSNPPCIANPMC) in complex with four nicotinic acetylcholine receptor (nAChR) subtypes: a3b2, a3b4, a6b2 and a6b4 nAChRs. For each system several files are provided: 1) an homology model that was used as a starting conformation is provided (eg 'a3b2_txd13.B99990023.pdb'),<br> 2) an Amber Parm7 topology file (eg 'a3b2_txd13_0023.prmtop'),<br> 3) a trajectory files containig 1250 frames extracted from a 100 ns molecular dynamics simulation (eg 'a3b2_txd13_0023_md_smaller.nc') created using pmemd from the Amber 18 package,<br> 4) the log file of this simulations (eg 'a3b2_txd13_0023_md.log'), and<br> 5) the coordinate file representing the minimized verion of the centroid frame of each simulation (with water and ions removed for conveniance) (eg 'a3b2_txd13_0023_md_centroid_min_nowat.pdb') The parameters used for the molecular dynamics simulations are provided in the 'md.in' file. All the text files have been compressed in the 'xz' format