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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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OPM and pdb2pqr #321

Open khelmy55 opened 2 years ago

khelmy55 commented 2 years ago

Why the pre-treated pdb files with OPM do not work with pdb2pqr?

sobolevnrm commented 2 years ago

What is OPM?

khelmy55 commented 2 years ago

Orientation of protein in membranes - it adds dummy atoms in the end of the pdb file, i thought this could be the reason why the treated pdb does not work with pdb2pqr, but it wasn't.

jbardhan commented 2 years ago

Hello,

Are you using structures from here? https://opm.phar.umich.edu/

Thanks very much, Jay

khelmy55 commented 2 years ago

Hello,

Yes, I am

jbardhan commented 2 years ago

ok, thank you! I would also have guessed that the DUM files are the issue. Can you please upload an example of what's not working, including both the apbs.in and PDB?

Thanks very much, Jay