I am a novel user, and although with some help of this platform I have made some progress in preparing my files for 2 molecule interactions, I am now faced with difficulties with using multiple molecules. My aim is to dock a putative epitope of a protein (PDB structure present, 2 chains (AB), coiled coils) onto my antibody. Via SAbPred, I have generated HC and LC PDB files of this antibody. Docking either HC or LC on one of the chains A or B of my protein works.
When I try to submit LC, HC and A, these come through without errors. However, I do not get through the input parameters.
I have tried the following:
- leaving the active residues field blank for all, or for any of the three
- indicating CDRs for the HC and LC, and putative 50 aa stretch containing epitope for A, and indicating for HC and LC that these interact with A and for A they interact with LC and HC
- in addition to the above, as a second active/passive residues input field opens with multiple molecules, I indicated as above, and in the scond input field for HC and LC the entire sequence for possible interaction with each other. In addition, I separately indicated the epitope of A to interact with HC and LC in the two selection#x input fields.
Nevertheless, I fail to pass to submit. The tutorials are currently offline, I do not get error messages and the sidenotes don’t really help me.
I hope I can get some relevant info here.
Kind regards, and thank you for your effort,