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

<p>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:</p> <p>1) an homology model that was used as a starting conformation is provided (eg&nbsp;&nbsp; &#39;a3b2_txd13.B99990023.pdb&#39;),<br> 2) an Amber Parm7 topology file (eg &#39;a3b2_txd13_0023.prmtop&#39;),<br> 3) a trajectory files containig 1250 frames extracted from a 100 ns molecular dynamics simulation (eg &#39;a3b2_txd13_0023_md_smaller.nc&#39;) created using pmemd from the Amber 18 package,<br> 4) the log file of this simulations (eg &#39;a3b2_txd13_0023_md.log&#39;), 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 &#39;a3b2_txd13_0023_md_centroid_min_nowat.pdb&#39;)</p> <p>The parameters used for the molecular dynamics simulations are provided in the &#39;md.in&#39; file.</p> <p>All the text files have been compressed in the &#39;xz&#39; format</p>