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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Protonation of histidine #322

Closed kexul closed 1 year ago

kexul commented 1 year ago

Dear pdb2par developers: I used the pdb2pqr server to prepare the pdb 7VTH for molecular dynamics simulation. After protonation, the H163 residue cannot form a hydrogen bond with the ligand anymore. Are there parameters I can tune to restore the hydrogen bond shown in the cocrystal structure? Thanks!

Before protonation:

企业微信截图_1113255f-0934-4b1d-a861-5b722655ff55

After protonation:

企业微信截图_a14ea8ea-2701-49d3-b295-46ac5b925c8a

Here is the .pqr file retrieved from the pdb2pqr server: kso6k3g3sa.pqr.txt

kexul commented 1 year ago

As the documentation said:

PDB2PQR has the ability to recognize certain protonation states and keep them fixed during optimization. To use this feature manually rename the residue name in the PDB file as follows:

I've tried modifying the residue name to HIE manually, it did work. But this needs some knowledge beforehand, is it possible to determine the best titration state of histidine automatically? Maybe use the information from the ligand? I've tried the --ligand option, but with no luck.