Hi,
I would like to dock with LigandFit a polypeptide. When the formal charges are computed, I obtained -1/2 on each oxygen for a carboxylate group. I thought such electron delocalization was correct but LigandFit refused to perform the docking process. It runs only with integer formal charge. Moreover, I can't save this molecule with such formal charges as mol file. However, the partial charges bear by both oxygens are the same.
If I modified the formal charges by zero and -1 on the respectively oxygens, it works, but I'm not satsfied with this !
- Why does LigandFit needs only integer as formal charges ? Where is it use in the docking process ?
- Is there a way to keep such charges and run LigandFit ?
Thank you.
I would like to dock with LigandFit a polypeptide. When the formal charges are computed, I obtained -1/2 on each oxygen for a carboxylate group. I thought such electron delocalization was correct but LigandFit refused to perform the docking process. It runs only with integer formal charge. Moreover, I can't save this molecule with such formal charges as mol file. However, the partial charges bear by both oxygens are the same.
If I modified the formal charges by zero and -1 on the respectively oxygens, it works, but I'm not satsfied with this !
- Why does LigandFit needs only integer as formal charges ? Where is it use in the docking process ?
- Is there a way to keep such charges and run LigandFit ?
Thank you.
