pdb2pqr modifies the chain names

[ndonyapour]

Hello, I'm utilizing pdb2pqr to add hydrogens to my structure with the following arguments.

pdb2pqr --ff='AMBER' --ffout='AMBER' --with-ph=7.0 --drop-water  --pdb-output complex_h.pdb receptor_pdb4amber.pdb complex_h.pqr

However, I observed that in the output files, the chain IDs have been changed. The original structure has one chain, whereas the output file has two chains where the chain B is the first one. I'm wondering if there's a way to preserve the original chain IDs and counts.

I really appreciate your help!

input.zip

[jbardhan]

Hi,

Thank you for the input.zip file and precise command you ran. I was able to reproduce the behavior.

Please note that I am not one of the main developers of pdb2pqr, so what I say here is my best attempt to understand what's happening in the code and what you might do. Others may weigh in to correct me or provide additional suggestions!

It looks to me as though there is no immediate way to keep the chain IDs exactly as they are in your input file. PDB2PQR takes note of termini and defines the chains accordingly. Because your residue 123 is the C terminus of a chain, it automatically separates the two and creates distinct chain IDs.

I haven't yet tested this understanding by modifying the code but will do so and report back.

Thanks very much,
Jay

[jbardhan]

Hi,

A small update: I thought there might be a small edit that could be made to the code that would generate the results you're asking for. However, making this change led me to find several other errors which will be impractical for me to fix.

As a result, I recommend a manual post-processing script to ensure that all atoms have the original chain ID. I am sorry I can't do more at this time, will make a note of this request.

Best regards,
Jay

[ndonyapour]

Hi,
Thank you for your effort and response! I fixed the issue by removing the OXT atom from the residue 123 but it would be great to have the option to retain the original chain IDs.

ATOM    998  OXT THR A 123     -14.250  17.212  21.346  1.00  0.00           O  

Best regards,
Nazanin

[jbardhan]

Ah, very good! Thanks for letting me know you're all set now. I see where this would be valuable and have recorded the suggestion as a possible modification.

Best regards,
Jay