Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 02)

<p>Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling</p> <p>Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3.</p> <p><strong>Instruction</strong></p> <p>The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example,</p> <p>`tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.`</p> <p>They can be decompressed with&nbsp;</p> <p>`cat Nolig_Respawn00a.tar.* | tar xzpvf -`</p> <p>&nbsp;</p> <p>&nbsp;</p> <p><strong>Remarks</strong></p> <ul> <li>Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model.</li> <li>There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&amp;l=list&amp;p=1&amp;s=10&amp;sort=newest</li> <li>For trajectories&nbsp;<em>without</em> keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands.&nbsp;For<em>`*</em>fitted<em>*</em>.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only.&nbsp;</li> </ul> <p>&nbsp;</p> <p>Please cite us if you find this data useful!</p>