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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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tetrahedral hydrogen reconstruction issue #336

Open sunghh44 opened 1 year ago

sunghh44 commented 1 year ago

Hi all,

I am trying to use the pdb2pqr server to solve the binding energy between macromolecules. I have 2 questions about APBS-PDB2PQR server.

  1. I want to calculate the electrostatic energy between p53 and mdm2 (PDB code 1ycr) using APBS server, as in the "Protein-RNA binding linked equilibria" example. The scale of the gradient of the electrostatic energy(dG/dlogSalt) is plausible(~ -1 kcal/mol). However, the scale of the electrostatic energy (~-50 kcal/mol) is much higher than I expected (-10 kcal/mol). therefore, the calculated binding affinity (~10^38 M-1) is unexpected higher than the experimental affinity (~10^8 M-1)

Could you explain the reason for the unexpected high electrostatic energy? Or should I use only the dG/dlogSalt value?

  1. I am trying to calculate the electrostatic energy between DNA and protein (PDB code 7vo0). However, the pdb2pqr server cannot produce the PQR file of DNA-only PDB file. Here are the warning messages of the DNA-only PDB file.

WARNING:Tetrahedral hydrogen reconstruction not available for nucleic acids. Some hydrogens may be missing (if so, this is a bug). WARNING:Suppressing further "Tetrahedral hydrogen reconstruction" messages

How can I solve this error? I am attaching the DNA-only PDB file to this post.

Best regards,

Sunghyun Hong Seoul National University,

DNA.zip