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The main requirement is to have structures files with good resolution. According to RSCB PDB documentation: Resolution is a measure of the quality of the data that has been collected on the crystal containing the protein or nucleic acid. The figure bellow is an example of how the resolution indicates the quality of the structure (linked from original ...


8

HADDOCK HADDOCK is both a web service and a standalone code. From the web server: HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or ...


5

Not a full answer, and it's too big for as a comment, but I can explain the linefix charge all qeq/reax 1 0.0 10.0 1.0e-6 reax/c. This function uses the charge equilibration method (QEq) from Rappe and Goddard (https://doi.org/10.1021/j100161a070) to calculate the partial charges on each atom in the simulation. It's not moving anything in the simulation and ...


5

Another factor to consider might be blind docking or targeted. In this latter, only a region indicated on protein is targeted. In blind docking, the ligand will bind wherever suited on the protein while in targeted only the region indicated will be accessible to the ligand. Blind docking is closer to the real biological setting but computationally expensive. ...


4

Packmol is used to pack molecules into a given box at random positions and with random rotations. If you want the spike glycoprotein to be attached to the membrane, you should probably prepare a new structure containing the two molecules as a single unit which Packmol won't break. Now you have achieved your goal. Next, you can use packmol for what it's ...


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