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ccsb-scripps / ADCP

AutoDock CrankPep for peptide and disordered protein docking
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ADCP error. The at is "NoneType" in clusterADCP.py line 182 #6

Open snowline opened 1 year ago

snowline commented 1 year ago

[bowei@localhost tar1]$ adcp -t 012_48e65_relaxed_rank_1_model_4_h.trg -s npisdvd -N 2 -n 10 -o 012_48e65_relaxed_rank_1_model_4_h_dock -ref 012_48e65_relaxed_rank_1_model_4_h.pdb Detected 8 cores, using 8 cores copying the ramaprob.data file from /home/bowei/ADFRsuite-1.0/CCSBpckgs/ADCP/ramaprob.data to /mnt/work/tar/tar1 Performing search (2 ADCP runs with 10 steps each) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| Docking performed in 8.02 seconds, i.e. 0 hours 00 minutes 08.020246 seconds Traceback (most recent call last): File "/home/bowei/ADFRsuite-1.0/CCSBpckgs/ADCP/runADCP.py", line 464, in runner(kw) File "/home/bowei/ADFRsuite-1.0/CCSBpckgs/ADCP/runADCP.py", line 406, in call runner(kw) File "/home/bowei/ADFRsuite-1.0/CCSBpckgs/ADCP/clusterADCP.py", line 182, in call modelAtomIndices.append(at.getIndices()[0]) AttributeError: 'NoneType' object has no attribute 'getIndices'

Is there anyone can help us? thanks!!!!

qoraj commented 1 year ago

Hello!

I am having the same problem. The tutorials and everything worked fine, but i am getting the same error as you guys:

~/ADFR10/bin/adcp -t mthk.trg -s npisdvd -N 20 -n 1000000 -o mthk_docking_ctx -ref mthk_poreH.pdb Detected 8 cores, using 8 cores copying the ramaprob.data file from /home/denis/ADFR10/CCSBpckgs/ADCP/ramaprob.data to /mnt/c/Users/denis/Documents/PhD/mthk/bioinformatics/ADCP_docking Performing search (20 ADCP runs with 1000000 steps each) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| Docking performed in 165.40 seconds, i.e. 0 hours 02 minutes 45.404079 seconds Traceback (most recent call last): File "/home/denis/ADFR10/CCSBpckgs/ADCP/runADCP.py", line 464, in runner(kw) File "/home/denis/ADFR10/CCSBpckgs/ADCP/runADCP.py", line 406, in call runner(kw) File "/home/denis/ADFR10/CCSBpckgs/ADCP/clusterADCP.py", line 182, in call modelAtomIndices.append(at.getIndices()[0]) AttributeError: 'NoneType' object has no attribute 'getIndices'

Did you solve the problem already?

kaplajon commented 1 year ago

It seems to be some kind of mismatch with the reference. I'm also just a user, but could it be that the reference and target structures are not of equal length? Hydrogens? I haven't used ADCP with a reference myself.

liszt-c commented 1 year ago

I think it was a mistake in the docking result. The problem in this step should be the comparison between the docking result and the original structure. I found that the docking result lacked some groups relative to the original peptide structure when this mistake occurred. When using ADCP, only a few peptides were able to docking successfully, and I still don't have a solution.

humblebeebio commented 8 months ago

I think you may be using your receptor as your reference when it should be your peptide structure. I had the same issue and error code. Using the peptide structure (the peptide pdbqt file) worked for me.