PDB2PQR error with heme ligand

[MR3300]

Hi,

I keep running into the same error, both running pdb2pqr locally and through the server. I am trying to calculate electrostatic surfaces for a heme containing protein.

I extract and generate a .mol2 file for the heme ligand (HEC) using PRODRG, removing the iron atom and adding hydrogens beforehand and include this along with the .pdb file for the whole protein (+ HEC) when submitting the job either locally or on the server. In both cases this is the error I get back:

"CRITICAL:Residue HEC 105 charge is non-integer: 34.8618 CRITICAL:Giving up."

Which I suspect is the result of a previous warning:

WARNING:PDB2PQR could not identify the following residues and residue numbers as returned by PROPKA or PDB2PKA

WARNING: HEC NA A WARNING: HEC CGA A WARNING: HEC NB A WARNING: HEC NC A WARNING: HEC ND A WARNING: HEC CGD A

These same atoms are flagged earlier on in the log file:

INFO:Found NAR group: 828- NA 105-HEC (A) [ 44.854 26.575 7.169] N INFO:Found OCO group: 836- CGA 105-HEC (A) [ 45.165 23.630 12.392] C INFO:Found NAR group: 839- NB 105-HEC (A) [ 45.380 27.146 4.404] N INFO:Found NAR group: 847- NC 105-HEC (A) [ 44.378 29.757 4.719] N INFO:Found NAR group: 855- ND 105-HEC (A) [ 43.902 29.128 7.459] N INFO:Found OCO group: 863- CGD 105-HEC (A) [ 40.197 29.179 12.181] C

I've tried modifying names in the pdb and .mol2 file to no avail. Does anyone have any suggestions as to what else I could try?

Regards,

M

[jbardhan]

Hi M,

Could you please attach the input file you're using? (You'll need to change the file extension to .txt)

Thanks very much, Jay

[MR3300]

Hi Jay,

Here are the input files are the resulting error files. I've tried lots of combinations of renaming residues in the pdb and mol2 but they pretty much all give the same error. This is a single heme protein and once I've resolved the issue I'm hoping to expand this to multiheme cytochromes (one step at a time).

I have no doubt this is down to user-error but it you're able to point me in the right direction it'd be appreciated.

Run2_1hrc_processed_pdb.txt Run2_pdb2pqr.stderr.txt Run2_PRODRG_HEC_edit_MOL2.txt

[jbardhan]

Hello, thank you for sharing these!

I'll try as well. We have seen a few "non-integer" errors over the last few weeks -- it may not be just user error.

Thanks very much, Jay

[sobolevnrm]

The heme residue is the source of the non-integer charge. However, since the heme should be covalently bonded to the protein, there should also be modifications to the protein structure that aren't considered by PDB2PQR. In general, PDB2PQR is not able to handle covalently modified biomolecules. Sorry, but I do not think this is fixable.