problem of atom charges in protein PDB files

[yangkimm]

what is the PDB file format in oddt(RSC PDB, charmm PDB)?
I want to calculate interactions (salt bridge, hydrogen bonds, etc ) between a protein and a short peptide which obtained from MD simulations (charmm pdb formats). The peptide C-terminal is carboxyl group (COO-). but when I used the commands below:
ligand = next(oddt.toolkit.readfile('pdb', 'ligand.pdb'))
ligand.protein = True
ligand.atom_dict['isminus']
all atoms are false.
so how oddt decides the charge of atom in pdb format or what special pdb formats needed by oddt?

[mwojcikowski]

Pdb format does not always include charges, which is particular problem for ligands, I would suggest using another format better suited for small molecules such as sdf or mol2.

Additionally I would suggest not to use protein = True for small molecules too.

[yangkimm]

My ligand is a little peptide including 5 residues and its C-terminal is carboxyl group(COO-),but the O- atom's formal charge is neither minus nor plus. I think its a common problem for protein. So the correctness of salt bridges in interactions module is doubtful.

[mwojcikowski]

Can you upload a sample file I will try to look a at it next week to figure it out

[yangkimm]

This is a pdb file.
G5COO.txt

[yangkimm]

A_minius.txt
This is a small molecule mol2 file. The O- in carboxyl group(COO-) is also not correct.

[yangkimm]

Further, I used the test cases in the source code (test_interactions.py). My scripts are:
python

import oddt
from oddt import interactions
mols = list(oddt.toolkit.readfile('sdf','actives_docked.sdf'))
list(map(lambda x: x.addh(only_polar=True), mols))
rec = next(oddt.toolkit.readfile('pdb', 'receptor_rdkit.pdb'))
rec.protein = True
rec.addh(only_polar=True)
salt_bridges_count = [len(oddt.interactions.salt_bridges(rec, mol)[0]) for mol in mols]
salt_bridges_count
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
but the code in test_interactions.py line 84 is:
assert_array_equal(salt_bridges_count,
[6, 7, 5, 5, 6, 5, 6, 4, 6, 5, 4, 6, 6, 5, 8, 5, 6, 6,
6, 7, 6, 6, 5, 6, 7, 5, 5, 7, 6, 6, 7, 6, 6, 6, 6, 6,
6, 5, 5, 6, 4, 5, 5, 6, 6, 3, 5, 5, 4, 6, 4, 8, 6, 6,
6, 4, 6, 6, 6, 6, 7, 6, 7, 6, 6, 7, 6, 6, 6, 5, 4, 5,
5, 6, 6, 6, 6, 6, 6, 4, 7, 5, 6, 6, 5, 6, 6, 5, 6, 5,
6, 5, 5, 7, 7, 6, 8, 6, 4, 5])
The files of actives_docked.sdf and receptor_rdkit.pdb are in the oddt-0.6/tests/data/dude/xiap directory, while the file of test_interactions.py is in the oddt-0.6/tests/ directory.