PDB2PKA as an alternative to PROPKA for calculating pH values used to protonate residues. This feature is EXPERIMENTAL. The libraries to make this feature available are included in the binary releases. They are NOT included in the source code and are not compiled with the rest of PDB2PQR. ...
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules. Electrostatics/pdb2pqr’s past year of commit activity Python1373850(2 issues need help)1UpdatedMar 2, 2025 apbs-awsPublic APBS in an AWS environment ...
These are notes for the current version of PDB2PQR Please see http://www.poissonboltzmann.org/pdb2pqr/release-history for the complete release history NEW FEATURES Replaced the Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 BUG FIXES Adde...
I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site. I've tried to go about it in two ways but keep getting stuck. 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+...
1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it cannot run anyechamber to allocate the atomic charge to Mn2+. Am i missing an update? Is there any way to get around this? Can I run ...
Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider...