sobolevnrm
commented
2 years ago Can you please provide the PDB and MOL2 file that generated the problem? Thank you.
Open rubinanoor9 opened 2 years ago
sobolevnrm
commented
2 years ago Can you please provide the PDB and MOL2 file that generated the problem? Thank you.
rubinanoor9
commented
2 years ago Kindly find the attach file
Hi pdb2pqr user! I have complex structure of receptor and ligand in the pdb format. I am trying to convert this pdb file into pqr file format for binding energy calculation. During running command line: pdb2pqr30 --ff=AMBER complex.pdb complex.pqr --ligand=lig.mol2
I got following error: INFO:PDB2PQR v3.5.2: biomolecular structure conversion software. INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). INFO:Checking and transforming input arguments. INFO:Loading topology files. INFO:Loading molecule: complex.pdb INFO:Setting up molecule. WARNING:Unable to find amino or nucleic acid definition for MN. Parsing as new residue. WARNING:Unable to find amino or nucleic acid definition for MN. Parsing as new residue. WARNING:Unable to find amino or nucleic acid definition for MOL. Parsing as new residue. INFO:Created biomolecule object with 372 residues and 5787 atoms. INFO:Setting termini states for biomolecule chains. INFO:Loading forcefield. INFO:Loading hydrogen topology definitions. INFO:This biomolecule is clean. No repair needed. INFO:Updating disulfide bridges. INFO:Debumping biomolecule. INFO:Adding hydrogens to biomolecule. INFO:Debumping biomolecule (again). INFO:Optimizing hydrogen bonds INFO:Applying force field to biomolecule states. INFO:Processing ligand. WARNING:Using ZAP9 forcefield for ligand radii. Traceback (most recent call last): File "/home/rubina/miniconda3/bin/pdb2pqr30", line 8, in
sys.exit(main())
File "/home/rubina/miniconda3/lib/python3.7/site-packages/pdb2pqr/main.py", line 822, in main
if main_driver(args) == 1:
File "/home/rubina/miniconda3/lib/python3.7/site-packages/pdb2pqr/main.py", line 790, in main_driver
is_cif=is_cif,
File "/home/rubina/miniconda3/lib/python3.7/site-packages/pdb2pqr/main.py", line 665, in non_trivial
ligand.assign_parameters()
File "/home/rubina/miniconda3/lib/python3.7/site-packages/pdb2pqr/ligand/mol2.py", line 330, in assign_parameters
self.assign_charges()
File "/home/rubina/miniconda3/lib/python3.7/site-packages/pdb2pqr/ligand/mol2.py", line 348, in assign_charges
atom.charge = atom.formal_charge
File "/home/rubina/miniconda3/lib/python3.7/site-packages/pdb2pqr/ligand/mol2.py", line 236, in formal_charge
nonbonded = NONBONDED_BY_TYPE[self.type]
KeyError: 'C'
and when we eliminate mol2 file of the ligand and use command line; pdb2pqr30 --ff=AMBER complex.pdb complex.pqr It generate pqr file of only protein residues and they also does not consider MN (manganese) in it. I am looking forward to hear from you. Thanks in adavance Regards
Rubina