ligand_gaff.pdb not being created

[agarrubio]

Hi! I need help with some issues. I am using https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Protein_ligand.ipynb. I am assuming that it is self contained. If I am supposed to run another jupyter before this one, please let me know! In the cell called Parameters to generate the protein topology, I get the following errors:

cat: /content/drive/MyDrive/make_it_rain/inputs/ligand_gaff.pdb: No such file or directory
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-14-482de45e3de6> in <cell line: 164>()
    162         vol = float(line.split()[1])
    163 
--> 164 vol_lit  = vol * pow(10, -27)
    165 atom_lit = 9.03 * pow(10, 22)
    166 conc = float(Concentration)

NameError: name 'vol' is not defined

The first one indicates that ligand_gaff.pdb is not being created. Here is a listing of the files in Google_Drive_Path:

total 548
-rw-rw-r-- 1 alejandro alejandro 125064 Dec  6 18:49 protein_ligand.pdb
-rw-rw-r-- 1 alejandro alejandro    797 Dec  6 18:49 tleap.in
-rw-rw-r-- 1 alejandro alejandro   4378 Dec  6 18:49 ligand_h.pdb
-rw-rw-r-- 1 alejandro alejandro      0 Dec  6 18:49 ligand_h_sslink
-rw-rw-r-- 1 alejandro alejandro   4455 Dec  6 18:49 ligand_h_nonprot.pdb
-rw-rw-r-- 1 alejandro alejandro     25 Dec  6 18:49 ligand_h_renum.txt
-rw-rw-r-- 1 alejandro alejandro 125095 Dec  6 18:47 starting_end.pdb
-rw-rw-r-- 1 alejandro alejandro      0 Dec  6 18:47 starting_end_sslink
-rw-rw-r-- 1 alejandro alejandro      0 Dec  6 18:47 starting_end_nonprot.pdb
-rw-rw-r-- 1 alejandro alejandro   5050 Dec  6 18:47 starting_end_renum.txt
-rw-rw-r-- 1 alejandro alejandro 125099 Dec  6 18:47 starting1.pdb
-rw-rw-r-- 1 alejandro alejandro    277 Dec  6 18:47 prepareforleap.in
-rw-rw-r-- 1 alejandro alejandro   5103 Dec  6 18:47 ligand_H.pdb
-rw-rw-r-- 1 alejandro alejandro   6028 Dec  6 18:46 phytate.pdb
-rw-r--r-- 1 alejandro alejandro 120461 Dec  5 22:26 mpnn68.pack.pdb

mpnn68.pack.pdb and phytate.pdb are my protein and ligand, respectively. Several of the files have zero size, which I don't know if is expected. What could be the cause of these errors? How can I debug this? Thanks, in advance, for your help!

[kadhirmn]

I'm also facing the same issue, sir, kindly help with this.

[pablo-arantes]

Hello everyone,

I have resolved the issues with the code. Please try running it again and inform me if it functions correctly.

Thank you.

Best regards,

[agarrubio]

Issue still remains in https://colab.research.google.com/github/pablo-arantes/making-it-rain/blob/main/Protein_ligand.ipynb

cat: /content/drive/MyDrive/make_it_rain/ligand_gaff.pdb: No such file or directory
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
[<ipython-input-9-c3fc94dbdbd3>](https://localhost:8080/#) in <cell line: 159>()
    157         vol = float(line.split()[1])
    158 
--> 159 vol_lit  = vol * pow(10, -27)
    160 atom_lit = 9.03 * pow(10, 22)
    161 conc = float(Concentration)

NameError: name 'vol' is not defined