Hey all, I am using the PyRx version (.8 and earlier free version). I am looking to do virtual screening of 2000+ ligands to my target molecule. I have all molecules in a sdf format inside a folder. When I go to input the ligands with the File,import, Chemical Table File-SDF. I then select my folder and select all 2000+ ligands at once. However, it only uploads the first ligand in the folder even if all are selected. When I do it one by one I am able to import multiple ligands. However, this would be way too time consuming.
Anyone have a fix for this issue?
You may try to compress that folder as a zip or gz file and then try to import in PyRx. I am not sure Pyrx does accept zip/gz format or not. If not, you can try another option, use OpenBable software (open-source) input all sdf files and make a single sdf file of all your compounds.
Hello Brandon Havranek, I have also faced the same problem what you are facing right now. You can try what Kazi Amirul Hossain has suggested, and surely you have to create a single SDF library for your 2000+ ligands to perform virtual screening. To build a single SDF library, you must have Open Babel software (Download link in the bottom). While using Open Babel, you must follow these steps:
Let me know if anything is unclear.
To Download Open Babel: http://openbabel.org/wiki/Main_Page
Thank you all Rameez Jabeer Khan Kazi Amirul Hossain your suggestions worked great!
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