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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Processing single chain vs multichain models #145

Closed rediaz111 closed 2 years ago

rediaz111 commented 2 years ago

Is there documentation on how multichain models affect pKa calculations? I obtained different pKa values for residues in Chain A when I submitted a single chain model vs when using a multichain model.

sobolevnrm commented 2 years ago

Any structure with multiple chains should behave differently than a single chain in isolation since multiple chains can change the solvent accessibility and charge environment of a titratable site.