Input files for PHY542 MD Practical

Name	Last modified	Size

Parent Directory		-
1ake_a.pdb	2016-11-15 23:58	130K
1ake_nowater.psf	2016-11-15 17:27	771K
1ake_nowater.xtc	2016-11-15 23:19	12M
4ake_a.pdb	2016-11-15 23:58	129K
adk.psf	2016-11-15 23:58	910K
adk_dims.dcd	2016-11-15 23:58	3.7M

See the Practical on molecular dynamics analysis with VMD for notes on these files. Download them to your local machine and then load them into VMD.

Trajectories

adk

Topology file adk.psf with trajectory adk_dims.dcd contains a dynamic importance (DIMS) MD simulation of apo AdK transitioning from the closed state (PDB ID 1AKE) to the open conformation (4AKE). The trajectory was taken from the paper O. Beckstein, E. J. Denning, J. R. Perilla, and T. B. Woolf. Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open/closed transitions. J. Mol. Biol., 394(1):160-176, 2009. doi: 10.1016/j.jmb.2009.09.009.

1ake_nowater

Topology file 1ake_nowater.psf with trajectory 1ake_nowater.xtc are the first 240 ns (1000 frames) from 1ake_009-nowater-core-dt240ps.dcd (see MDAnalysis Workshop Data Download for obtaining the original trajectories).

The trajectory contains frames from am equilibrium simulation of adenylate kinase starting from the closed (apo) conformation (PDB ID 1AKE with ligand removed) with the CHARMM27 force field and the TIP3P water model, performed on the PSC Anton super computer by Sean Seyler. The trajectory only contains the protein; all solvent was stripped.