I am calculating binding affinity of protein-ligand complex. I submitted two jobs in last week and the links are in below.
https://wenmr.science.uu.nl/prodigy/run/nfV_3Nq-%2B8rB
Still I see jobs are running from link. I did not receive any email whether jobs are completed. According to my understanding those jobs should not take long time. Could you please suggest your opinions and those are very helpful for me.
Thank you very much for your valuable time and help,
Have a nice day,
Thanks for reporting this issue.
Indeed it should not take this long, there was an error in your processing that is not being correctly handled by the server.
The errors were:
# nfV_3Nq-+8rB
ERROR: Ligand identifier LIG found 10 times in chain B of the input file. Please remove the redundant molecule(s).
# nfV_3Nq+S36M
ERROR: Ligand identifier LIG found 9 times in chain B of the input file. Please remove the redundant molecule(s).
We will fix this so that these error are displayed in the server, in the meanwhile; try to address this error message and re-submit.
Thank you very much for your valuable suggestions. With the help of those, I am able to run and calculate ΔG for the different systems. I have one questions. Can I calculate ΔH or ΔS (any of the quantity) using PRODIGY and could you please suggest your opinion that is very helpful for me. Thank you so much for your valuable time and help. Have a nice day. Maiti
Prodigy was not trained to calculate dG and dS - even if you were to calculate it at different temperatures I would not trust that you can extract dH and dS
Happy to hear its working now, please let us know if you find any other issues! 