Some of the protonation states derived from the [PROPKA]] results are not supported in the requested forcefield and thus PDB2PQR is unable to get charges and radii for that state. PDB2PQR currently supports the following states as derived from PROPKA:
| Protonation State | AMBER Support | CHARMM Support | PARSE Support |
|---|
| Neutral N-Terminus | No | No | Yes |
|---|
| Neutral C-Terminus | No | No | Yes |
|---|
| Neutral ARG | No | No | No |
|---|
| Neutral ASP | Yes† | Yes | Yes |
|---|
| Negative CYS | Yes† | No | Yes |
|---|
| Neutral GLU | Yes† | Yes | Yes |
|---|
| Neutral HIS | Yes | Yes | Yes |
|---|
| Neutral LYS | Yes† | No | Yes |
|---|
| Negative TYR | No | No | Yes |
|---|
† - only if residue is not a terminal residue; if the residue is terminal it will not be set to this state |
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