Hello,
My problem is the following:
In LigandFit, we defined a binding site in which 23 compounds will be docked. Among this training set, there is a molecule with an aromatic cycle with a bromide atom and another one with an aromatic cycle with Cl and F atoms.
Both molecules extrated from PDB files are well docked. The same molecules that were minimized and docked in the same binding site than previously yielded the following error message: "Ligand shape doesn't match any site".
We tried to replace F, Cl and Br atoms with CH3 groups and it is working. However if we replace such halogen atoms by hydrogen, it is not working (same error message than previously in the docking process).
Could you help me to solve this problem, please ?
Thank you.
My problem is the following:
In LigandFit, we defined a binding site in which 23 compounds will be docked. Among this training set, there is a molecule with an aromatic cycle with a bromide atom and another one with an aromatic cycle with Cl and F atoms.
Both molecules extrated from PDB files are well docked. The same molecules that were minimized and docked in the same binding site than previously yielded the following error message: "Ligand shape doesn't match any site".
We tried to replace F, Cl and Br atoms with CH3 groups and it is working. However if we replace such halogen atoms by hydrogen, it is not working (same error message than previously in the docking process).
Could you help me to solve this problem, please ?
Thank you.
