Protein_ligand.ipynb PDBFixer problem
zjun028 opened this issue · comments
Hello~~
I am using the is to process a small molecule PDB file, but I am observing unexpected behavior in the output file generated by the following two lines:
fixer = PDBFixer(filename=ligand_pdb)
PDBFile.writeFile(fixer.topology, fixer.positions, open("temp.pdb", 'w'))
To provide some context, I am working with a small molecule PDB file, specifically from DrugBank (DB09330, accessible at https://go.drugbank.com/structures/small_molecule_drugs/DB09330.pdb).
However, the resulting file (temp.pdb) contains only three atoms, significantly reduced from the complete structure:
HETATM 1 C UNK A 1 -2.426 5.262 0.000 1.00 0.00 C
HETATM 2 N UNK A 1 6.554 -2.962 0.000 1.00 0.00 N
HETATM 3 O UNK A 1 -1.434 1.654 0.000 1.00 0.00 O
I appreciate your time and assistance in resolving this issue. Thanks very much!
Maybe this is the reason:
openmm/openmm#2086
Hi @zjun028,
The issue is on the third column of your PDB file (atom name). You have the same atom name for several atoms. I changed and tried in the notebook and it worked well.
Follow what I did:
ATOM 1 C1 UNK 0 -5.435 -0.646 0.000 0.00 0.00 C
ATOM 2 C2 UNK 0 -5.435 -2.190 0.000 0.00 0.00 C
ATOM 3 N3 UNK 0 -4.096 -2.962 0.000 0.00 0.00 N
ATOM 4 C4 UNK 0 -2.773 -2.190 0.000 0.00 0.00 C
ATOM 5 N5 UNK 0 -2.773 -0.646 0.000 0.00 0.00 N
ATOM 6 C6 UNK 0 -4.096 0.126 0.000 0.00 0.00 C
ATOM 7 C7 UNK 0 -4.096 1.654 0.000 0.00 0.00 C
ATOM 8 N8 UNK 0 -1.434 -2.962 0.000 0.00 0.00 N
ATOM 9 C9 UNK 0 -0.110 -2.190 0.000 0.00 0.00 C
ATOM 10 C10 UNK 0 -2.852 2.552 0.000 0.00 0.00 C
ATOM 11 N11 UNK 0 -3.340 4.017 0.000 0.00 0.00 N
ATOM 12 C12 UNK 0 -4.868 4.017 0.000 0.00 0.00 C
ATOM 13 C13 UNK 0 -5.341 2.552 0.000 0.00 0.00 C
ATOM 14 C14 UNK 0 -5.892 5.167 0.000 0.00 0.00 C
ATOM 15 C15 UNK 0 -7.405 4.852 0.000 0.00 0.00 C
ATOM 16 C16 UNK 0 -7.877 3.387 0.000 0.00 0.00 C
ATOM 17 C17 UNK 0 -6.853 2.237 0.000 0.00 0.00 C
ATOM 18 C18 UNK 0 1.229 -2.962 0.000 0.00 0.00 C
ATOM 19 C19 UNK 0 2.552 -2.190 0.000 0.00 0.00 C
ATOM 20 C20 UNK 0 2.552 -0.646 0.000 0.00 0.00 C
ATOM 21 C21 UNK 0 1.229 0.126 0.000 0.00 0.00 C
ATOM 22 C22 UNK 0 -0.110 -0.646 0.000 0.00 0.00 C
ATOM 23 N23 UNK 0 1.229 1.654 0.000 0.00 0.00 N
ATOM 24 O24 UNK 0 1.229 -4.490 0.000 0.00 0.00 O
ATOM 25 C25 UNK 0 -0.110 -5.262 0.000 0.00 0.00 C
ATOM 26 N26 UNK 0 3.891 0.126 0.000 0.00 0.00 N
ATOM 27 C27 UNK 0 5.215 -0.646 0.000 0.00 0.00 C
ATOM 28 C28 UNK 0 3.891 1.654 0.000 0.00 0.00 C
ATOM 29 C29 UNK 0 5.215 -2.190 0.000 0.00 0.00 C
ATOM 30 N30 UNK 0 6.554 -2.962 0.000 0.00 0.00 N
ATOM 31 C31 UNK 0 6.554 -4.490 0.000 0.00 0.00 C
ATOM 32 C32 UNK 0 -0.110 2.426 0.000 0.00 0.00 C
ATOM 33 C33 UNK 0 -0.110 3.970 0.000 0.00 0.00 C
ATOM 34 O34 UNK 0 -1.434 1.654 0.000 0.00 0.00 O
ATOM 35 C35 UNK 0 1.229 4.726 0.000 0.00 0.00 C
ATOM 36 C36 UNK 0 7.877 -2.190 0.000 0.00 0.00 C
ATOM 37 C37 UNK 0 -2.426 5.262 0.000 0.00 0.00 C
I hope it helps.
Thank you.
Best,
Pablo