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12 votes

What are the factors to consider before docking 2 proteins?

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 ...
Camps's user avatar
  • 23.5k
8 votes

Which non-commercial software can be used to dock two proteins?

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 ...
Camps's user avatar
  • 23.5k
6 votes

What are the factors to consider before docking 2 proteins?

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 ...
BND's user avatar
  • 1,341
5 votes

Why am I losing bonds when I use PACKMOL on two proteins?

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 ...
Susi Lehtola's user avatar
  • 19.7k
5 votes

LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands

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 ...
Matt's user avatar
  • 351

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