test.pdbqt: the output PDBQT file prepared with meeko command:
mk_prepare_ligand.py -i test.sdf -o test.pdbqt
Here is the output.
REMARK SMILES C=O
REMARK SMILES IDX 1 1 2 2
REMARK H PARENT
REMARK Flexibility Score: inf
ROOT
ATOM 1 C UNL 1 1.051 0.087 -0.049 1.00 0.00 0.307 C
ATOM 2 O UNL 1 2.275 0.087 -0.049 1.00 0.00 -0.307 OA
ENDROOT
TORSDOF 0
There is no name line in the REMARK lines. Here is an example with Name line:
REMARK Name = test
REMARK 0 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL 1 1.051 0.087 -0.049 0.00 0.00 +0.000 C
ATOM 2 O UNL 1 2.275 0.087 -0.049 0.00 0.00 +0.000 OA
ENDROOT
TORSDOF 0
The name of a molecule is a very important information. But the output file of meeko did not include the name line.
test.sdf: an example of input file with molecular name "test"
test.pdbqt: the output PDBQT file prepared with meeko command:
Here is the output.
There is no name line in the REMARK lines. Here is an example with Name line: