Protonation States

The protonation states of Asp, Glu, His, Tyr, Cys, Lys, and phosphorylated residue side chains can vary depending on the pH and the local environment of the residue, and in principle more than one protonation state could have nontrivial populations under a given set of conditions. Clearly, utilizing an incorrect protonation state for a polarizable side chain can lead to substantial errors in the electrostatic energies, and thus incorrect predictions. The prediction of protonation states is still under development. Manual modification of protonation states is supported using the following command:

pka change residue type

where "residue" is a particular Asp/Glu/His residue, specified with the usual "chain:residue" format, and "type" is a 3 letter code (all caps) specifying which protonation state should be used. For the relevant codes, click here. As an example,

pka change A:123 HIP

would change the protonation state of residue 123 in chain A, which must be a histidine, to the doubly protonated, positively charged form. Note that the protonation states of the N-terminal amino and C-terminal carboxy groups cannot be modified at present (unfortunately).