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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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examples for parameterizing ligands #289

Open michaelmorgan937 opened 2 years ago

michaelmorgan937 commented 2 years ago

There are two examples (1HPX and 1ABF) of parameterizing ligands in the documentation. However, I failed at both. I used mol2 files obtained here (http://pdb2pqr.sourceforge.net/examples/), and also tried mol2 files generated by myself using VMD.

LIG_1HPX.mol2.txt 1HPX_pdb2pqr.stderr.txt LIG_1ABF.mol2.txt 1ABF_pdb2pqr.stderr.txt

Please help to instruct what I did wrong and how to correct them. Thank you very much.

intendo commented 2 years ago

@michaelmorgan937 I am sorry you are having problems. What version of pdb2pqr are you using? Can you send the command line arguments that you used to produce the output files?

michaelmorgan937 commented 2 years ago

@intendo I followed the document and tried both your server and downloaded version. The version information (which is 3.5.0) can be found in the stderr file I attached, as well as the error message.

sobolevnrm commented 2 years ago

This information was from a very old tutorial that I am in the process of deleting. The most recent documentation can be found at https://pdb2pqr.readthedocs.io/en/latest/.

michaelmorgan937 commented 2 years ago

@sobolevnrm they are pretty much the same. I followed the new documentation but used the mol2 files from the old one since the new documentation does not provide mol2 files. I also tried generating mol2 files by myself as I said in the original post. Can you provide a working mol2 file for the example? thanks.