Hi, I was trying to run Obminimize to convert SDF files that I converted from SMILE strings into PDBQT files, and when I run the code that I have to loop it with a perl script with multiple files, I'm constantly getting this error: "obminimize: cannot read input/output format!"
I was wondering if there might be any reason for this as I'm not very experienced with coding or open babel, and have attached my code and an example .sdf file that I have. I'm on the most updated Open babel there is, and Ive made sure to correctly place the files in the respective folders. I was wondering maybe if there was anything that I'm doing wrong that you guys could point out that I've unsuccessfully been able to perform? Cheers, Locke
import os
folder_path = "C:/Users/sahilmada/Desktop/BABEL" # Replace with the actual folder path
for filename in os.listdir(folder_path):
if filename.endswith('.sdf'):
input_file = os.path.join(folder_path, filename)
output_file = os.path.splitext(filename)[0] + '.pdbqt'
command = f'obminimize -o pdbqt -sd -ff GAFF -h {input_file} > {output_file}'
os.system(command)
untitled_line_2__input2.sdf
Description: Binary data
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