Hi all,
I need advise on an open-source web based reliable conformer generator for small molecule sugar ligands. I understand this platform is haddock related, but I have hit a roadblock in finding a good one. I have tried frog2 and neurosnap but the results were not accurate.
Thank you
Vibes
For generating glycans check the GLYCAM web server.
For generating ligand conformations from smile strings we have built a small tool for it.
Hi, I tried to execute the smiles2pdb command on windows command prompt. But it did not work, could you please advise on which platform I should run this command on?
You will have to install the Windows Linux Subsystem (WLS).
Hi, I installed WLS and tried a couple of things to get it running. But, it says smile2pdb command not found. I have no understanding about coding, could you please guide me on how to get it running? I will attach a screenshot for your reference.
There is no free lunch 
Try downloading a precompile executable from: https://www.dropbox.com/scl/fi/yr7rykhgp6c4u2dljsk6l/smiles2pdb?rlkey=0v3g8tc0s9t2zuhrjg2ue5csp&dl=0
You will have to make it executable on your WLS system with:
chmod +x smiles2pdb
Hi, thank you very much for your inputs. The code is running now. There in only one more thing. My structure is a sugar molecule in 1C4 confirmation. When I input the smiles string and convert it to pdb file using smiles2pdb command, it is returning my molecule in 4C1 or other distorted confirmation. Any tips or work around for this?
If you are dealing with sugars, check the GLYCAM web server
