Error when trying to get PST embedding

[AlyciaBHZ]

I am trying to get the PST embedding, however when I execute the following code:

dataset=YAP1_HUMAN_Fields2012-singles-linear 
a=0 
b=319
python3 src/PST_embedding.py $dataset $a $b

I got this:

Traceback (most recent call last):
  File "/TopFit/src/PST_embedding.py", line 97, in <module>
    runPST.main(feature_list,PDBid, Chain, mutations, num_sites, pH, ['WT','MT'],
  File "/TopFit/src/PST/runPST.py", line 71, in main
    pro_wt=pro_complex(PDBid, Chain, mutations,'WT')
  File "/TopFit/src/PST/PST_features.py", line 53, in __init__
    atoms_m_m,atoms_m_o = loadMutantPDB(PDBfile,muteChain,resID)
  File "/TopFit/src/PST/PST_features.py", line 128, in loadMutantPDB
    fp = open(PDBfile)
FileNotFoundError: [Errno 2] No such file or directory: '4rex_WT_A173.pdb'

This also keeps happening in my customized dataset, and it seems like asking for a specific mutated PDB file, how should I deal with this, thanks!

[YuchiQiu]

The code should generate the mutated PDB file. You need to install VMD and Jackal according to the instructions. If so, can you further check if you run code get_structure at Line 70 in scr/PST/runPST.py successfully?

[AlyciaBHZ]

Hi, thank you for your quick response, I think the problem lies in src/PST/PST_structure.py line 69: os.system('./scap -ini 20 -min 4 '+filename+'_WT.pdb tmp_scap.list') where gives the error: I tried chmod +x scap but this did not help, how can I possibly fix this, thanks!

[YuchiQiu]

You need to give permission to the directory to execute the program.