An error occured - pocket too large

[ntnn19]

Hi,

Thanks for your incredible tool.

I got the following error after trying to dock a ligand to a very large target protein (15 chains, >8,000 residues) that was predicted using AlphaFold 3:

Reading input ... done.                                                                     
Using pocket rank: 5                                                                        
Setting up the scoring function ... done.                                                   
Using heuristic search_depth                                                                
Analyzing the binding site ... done.                                                        
GPU Platform: NVIDIA CUDA                                                                   
GPU Device: NVIDIA RTX A6000                                                                
GPU Device: NVIDIA RTX A6000                                                                
Using random seed: 43918152                                                                 
                                                                                            
Build kernel 1 from source                                                                  
OpenCL version: 3.0                                                                         
                                                                                            
Build kernel 2 from source                                                                                                                                                              
OpenCL version: 3.0                                                                                                                                                                     
                                                                                            
                                                                                            
An error occurred: pocket too large!.                                                       
                                                                                            
Please contact the author, Jiansheng Wu <jansen@njupt.edu>, so                              
that this problem can be resolved. The reproducibility of the                               
error may be vital, so please remember to include the following in                          
your problem report:                                                                                                                                                                    
* the EXACT error message,                                                                  
* your version of the program,                                                              
* the type of computer system you are running it on,                                        
* all command line options,                                                                 
* configuration file (if used),                                                             
* ligand file as PDBQT,                                                                     
* receptor file as PDBQT,                                                                   
* flexible side chains file as PDBQT (if used),                                             
* output file as PDBQT (if any),                                                            
* input (if possible),                                                                      
* random seed the program used (this is printed when the program starts).                   
                                                                                            
Thank you!  

I was hoping to get some directions to possible workarounds.

Thank you!

[asarigun]

Hi,

I'm not sure what your box size is, but if none of the box dimensions (X, Y, or Z) exceed 30 Å, it shouldn't cause any error.