I can't seem to get an output on prodigy

PRODIGY
1

Hi! I would like some help.

I am trying to get the binding affinity between the CDRs of an antibody and the WHISCY active residues of an antigen. I used a ClusPro docked model as the input. I believe I submitted the job a few days ago, but it still seems to be running- which, I am guessing, something was wrong with the way I entered the information.

The docked structure from Cluspro had named the antibody as rec.pdb and the antigen as lig.000.00.pdb. Both the structures were present in a single file. Both the structures are labelled as chain A. I know the specific residue numbers for the CDRs and the active residues,

Is there a way I can obtain the dG for those specific residues?

I would really appreciate an help and or tips.

Thank you :slight_smile:

2

You have to assign different chainID to your antibody and antigen.

3

Hi, Thank you for your reply.

I tried that, but I still haven’t gotten an output. The run code is nGz_3PRYpQlh. I submitted the job about 24+hours ago.

4

There were some portal updates today.

Please try again.

And you might also try to run an example (to test that the server works - which will point to a problem in your input PDB)