For a project I need to first bind a certain carbohydrate (that we made with glycam) to a protein, and then make a complex of the protein+carbohydrate and LDLR. However to test if it runs in HADDOCK I tried to make a complex of the carbohydrate and my protein. But the OH group (which is necessary for the project) causes a problem. I get the following error:
Unable to generate topology for ligand ROH. PRODRG did not create the required output:
PRODRG>WARNING: deleted hydrogen HO1 from your input.
In SPDB Viewer the OH group makes a triangle with itself somehow (the H atoms form an extra bond with the nearby O and C atoms) which is why this error occurs I assume. Is there a way to solve this?