The current protonation software package, pdb2pqr, embedded in EnzyHTP cannot consider the bound ions. This causes serious issues in specific systems such as PafA (pdb id 5tj3). This enzyme contains two Zn2+ ions at the active site.
As shown on the top, the correct protonation of two histidines should be HID, which exposes the nitrogen atoms with partial negative charges (NE in both histidines) to the positive charge of Zn2+. However, the current automatic protonation function of EnzyHTP will protonate those two histidines as HIE, which exposes the partial positive charges to ZN2+. This causes the high electrostatic destabilization at the active site and the resulting constant flowing away of those two ZN2+ ions. The ZN2+ drifting causes the following AMBER error to constantly happen even after resubmission of the restart file:
"ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values."
(Note: The expression "periodic box dimensions have changed too much" is misleading. Constant increases of some specific atom distances such as the ZN2+ drifting not causing significant box dimension change can also cause this kind of error.")
The correct protonation of those two histidines can be achieved by H++, which could be a good alternative or complementation of pdb2pqr.
The current protonation software package, pdb2pqr, embedded in EnzyHTP cannot consider the bound ions. This causes serious issues in specific systems such as PafA (pdb id 5tj3). This enzyme contains two Zn2+ ions at the active site.
As shown on the top, the correct protonation of two histidines should be HID, which exposes the nitrogen atoms with partial negative charges (NE in both histidines) to the positive charge of Zn2+. However, the current automatic protonation function of EnzyHTP will protonate those two histidines as HIE, which exposes the partial positive charges to ZN2+. This causes the high electrostatic destabilization at the active site and the resulting constant flowing away of those two ZN2+ ions. The ZN2+ drifting causes the following AMBER error to constantly happen even after resubmission of the restart file:
"ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values." (Note: The expression "periodic box dimensions have changed too much" is misleading. Constant increases of some specific atom distances such as the ZN2+ drifting not causing significant box dimension change can also cause this kind of error.")
The correct protonation of those two histidines can be achieved by H++, which could be a good alternative or complementation of pdb2pqr.