I have been using the latest version of GOLD for docking ligand (Sugar substrate, GDP-Man) to the binding site of protein structure. After the docking process is completed, ligand is docked in the right place but the problem is that the conformations are inverted. The part that should be in acceptor site is seen in donor site and vice versa. It is not always the case, some of them are in right orientation and some are in wrong. Now, in that case, is there any way to define particular site to be in particular place so that every docked ligand would be in right orientation? I had heard some time that we can define such sites but I have not yet been able to do it. Actually I am using GOLD within Discovery Studio 3.0. If this option is not available or this operation is not possible with GOLD, could you suggest another docking program which would provide better results.
Thanking you in advance!