getting right protonation state from PKa of Rosie

[Anonymous]

Hello,

Does the pdb file in the output folder of pKa give us the right protonation state of pdb file?

Also, there are two options in pKa program in ROSEI:

1.Pack side chains and protonation states of the residues neighboring the target residue during pK_a calculations

2.Pre-pack the side chains and protonation states of all the residues in the input PDB before pK_a calculations

 

which one should  we use to get the right protonation state?

 

Thanks

[Author]

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