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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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the shell command shouw #228

Closed swdoctor closed 2 years ago

swdoctor commented 2 years ago

Dear pdb2pqr author :

the command line pdb2pqr30 show me give up, but in your website it works right.

My command is "pdb2pqr30 --titration-state-method=propka --with-ph=6.0 --ff=AMBER --ffout=AMBER ./T3_1u19_0_protein.pdb ./AAA.pqr"

The pdb documents in T3_1u19_0_protein.pdb.txt, you need move T3_1u19_0_protein.pdb.txt to T3_1u19_0_protein.pdb T3_1u19_0_protein.pdb.txt

jbardhan commented 2 years ago

Hi,

Just to check, this is the error you get from the command line?

CRITICAL:Residue WAT 964 charge is non-integer: -0.417 CRITICAL:Giving up.

Thanks very much, Jay

jbardhan commented 2 years ago

It looks like the use of multiple hydrogens named "HW" in the water residue is the culprit. The oxygen has a charge of -0.834 and the hydrogens each have +0.417.

To test this, I took out all the waters but 964, and changed the water hydrogen names to H1 and H2. After doing this, pdb2pqr30 ran successfully using the command you gave.

I'm a bit confused because the atom name "HW" seems to be appropriate for AMBER. As a result, I'm not sure why the code would fail on this, nor am I sure why it works on the website but not command line.

@intendo , can you please have a look at this? I'll keep looking at it as well.

Thanks very much, Jay

jbardhan commented 2 years ago

I am unable to get this working on the website either ( https://server.poissonboltzmann.org/ ) . Can you please share the jobID that succeeded, and ideally the date you submitted the job as well?

Thanks very much, Jay

sobolevnrm commented 2 years ago

There appears to be something wrong with the water molecules in this file. When I delete them, the problem goes away.

sobolevnrm commented 2 years ago

And the problem appears to be with the water hydrogens -- when I delete the hydrogens the run also completes without problem.

sobolevnrm commented 2 years ago

It looks like the use of multiple hydrogens named "HW" in the water residue is the culprit. The oxygen has a charge of -0.834 and the hydrogens each have +0.417.

To test this, I took out all the waters but 964, and changed the water hydrogen names to H1 and H2. After doing this, pdb2pqr30 ran successfully using the command you gave.

I'm a bit confused because the atom name "HW" seems to be appropriate for AMBER. As a result, I'm not sure why the code would fail on this, nor am I sure why it works on the website but not command line.

@intendo , can you please have a look at this? I'll keep looking at it as well.

Thanks very much, Jay

I've confirmed what @jbardhan mentioned above: the duplicate water hydrogen names are causing the problem. The attached version of the PDB works with PDB2PQR: T3_1u19_0_protein-fixed.pdb.txt