004 - roGFP2-oxd simulation

This experiment performs classical MD simulations of the oxidized form of roGFP2 for benchmarking structural changes of mseGFP mutations.

Protein preparation

We prepared the roGFP2 structure (PDB: 1JC1) with the protein preparation from RCSB protocol. The final structure is shown below with labels on the experiment's relevant residues.

Warning

Because the chromophore (CRO 65) is a non-standard residue, PDB2PQR does not place any hydrogens and are missing in 1JC0-final.pdb. Hydrogen atoms are added in the next protocol (tleap).

Production

Each frame represents a stride of 2.5 ns for a total of 100 ns.