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README.txt
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README.txt
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heme_b558.xyz, heme_b595.xyz, hemed.xyz are the coordinate files for the geometry optimized structures
tleap.in: Amber leap script to generate Amber rst7 and prmtop files
heme.lib: Amber residue library file with HB1 (heme b558), HB2 (heme b595), HDD (heme d), HIO (backbone for histidine), MTO (backbone for methionine), GUO (backbone for glutamate), PRN (deprotonated propionate), and PRP (protonated propionate)
heme.frcmod: Amber force field modification file with all parameters for each heme cofactor system
mcpbpy.frcmod: Amber force field modification file with all parameters between the metal and the axial ligands for each heme cofactor system, generated by MCPB.py
6rko_final.pdb: PDB 6RKO with missing residues 240-248 and 334-339 in chain A modelled using Maestro and missing atoms in POPC lipids added back using CHARMM-GUI
protein.pdb: 6rko_final.pdb in Amber format (renumbered)
protein_solv.pdb: protein.pdb solvated with TIP3P water molecules and counterions (ionic strength = 0.10 M)
protein_solv_equil.pdb: protein_solv.pdb equilibrated (minimization, heating, and equilibration for 10 ns)
ubiquinone was modelled with generalized Amber force field (GAFF)
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In order to execute the Amber LEeaP script:
tleap -f tleap.in