PDBFixer not working some PDB file

[AhmetGG]

Hi,

Before running Openmm, I would like to edit some protein structure via PDBFixer. But while Fixer read some PDB, some are not read. What can I do in order to be read PDB structure? By the way PDB structure is a predicted model not cystral.

[swails]

Without providing the PDB file that causes the problem there's really no way to diagnose. If there's a PDB from RCSB that fails to parse, you can just provide the code. Otherwise, can you attach it here so we can try to reproduce the problem?

[AhmetGG]

Thank you so much for replying.I added this unreaded file in the following: T1084.txt I couldnt put this file as pdb so I can put it as txt.

[peastman]

Your file begins with several lines that aren't part of the PDB format.

PFRMAT TS
TARGET T1084
MODEL 1
PARENT N/A

You need to remove those lines, or else prefix each one with "REMARK" to indicate that it's a comment.

[raoufkeskes]

for me fixer.addMissingAtoms() it is not working and showing KeyError: 'NDG' the pdb code is : 3iyw

[Zuricho]

for me fixer.addMissingAtoms() it is not working and showing KeyError: 'NDG' the pdb code is : 3iyw

I found a solution for your problem:

# replace nonstandard residues
fixer.findNonstandardResidues()
fixer.missingResidues = {}
fixer.replaceNonstandardResidues()

Set the missingResidues as blank, and continue with removeHeterogens will work.