# PRODIGY Error running my PDB file containing my docked proteins from ClusPro

**URL:** <https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418>\
**Category:** PRODIGY\
**Created:** [July 17, 2023, 12:39pm UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418 "2023-07-17T12:39:54Z")\
**Posts on this page:** 20\
**Page:** 1

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**Author:** ![metanoia](https://avatars.discourse-cdn.com/v4/letter/m/7c8e57/32.png) [@metanoia](https://ask.bioexcel.eu/u/metanoia)\
**Post date:** [July 17, 2023, 12:39pm UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/1 "2023-07-17T12:39:54Z")

</div>

![Screenshot 2023-07-17 203456](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/cad990811d27d912acf2c1a6572c0af156d63114.png)  
Been trying to get the binding energy of my protein complex, Ligand shown in Red, receptor in green. PyMol showed that there polar contacts on my protein but it seems prodigy is having errors. Prodigy error log says no contacts

Prodigy error log also says there are gaps in residue fragments. But these gaps were already within the PDB files from where I got the structures from. I didn’t change nor edit the structures myself. Only used what was deposited in PDB.

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [July 17, 2023, 12:52pm UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/2 "2023-07-17T12:52:39Z")

</div>

Did you define the correct chains for use in PRODIGY?

Please provide details (e.g. PDB code and chain definition you used)

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<div class="post-metadata">

**Author:** ![metanoia](https://avatars.discourse-cdn.com/v4/letter/m/7c8e57/32.png) [@metanoia](https://ask.bioexcel.eu/u/metanoia)\
**Post date:** [July 17, 2023, 1:07pm UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/3 "2023-07-17T13:07:49Z")

</div>

Since this was from the docking models of ClusPro2.0, The ligand and receptor I used were from [RCSB PDB - 6CM4: Structure of the D2 Dopamine Receptor Bound to the Atypical Antipsychotic Drug Risperidone](https://www.rcsb.org/structure/6cm4) for the dopamine receptor (green) and [RCSB PDB - 7LLL: Exendin-4-bound Glucagon-Like Peptide-1 (GLP-1) Receptor in complex with Gs protein](https://www.rcsb.org/structure/7LLL) for the exendin-IV ligand (red).

I basically removed all other proteins from their respective PDB files and only isolated the protein and receptor that I needed.

Thank you for the speedy reply, PRODIGY team!

Here is the complete error log of my run:

# ===========================================================================

command: /usr/local/bin/prodigy DRD2\_Exendin\_IV\_cluspro.pdb --selection A B,C,D,E,F,G --temperature 25.0 --contact\_list --pymol\_selection  
exit status: 1  
log:  
[+] Reading structure file: /data/runs/3RTCqPXS/DRD2\_Exendin\_IV\_cluspro.pdb  
[!] Structure contains gaps:  
R TYR34 \< Fragment 0 \> R THR225  
R GLN365 \< Fragment 1 \> R LEU441  
P HIS1 \< Fragment 2 \> P ASN28

[+] Parsed structure file DRD2\_Exendin\_IV\_cluspro (2 chains, 297 residues)  
Traceback (most recent call last):  
File “/usr/local/bin/prodigy”, line 8, in   
sys.exit(main())  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 421, in main  
prodigy.predict(  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 154, in predict  
self.ic\_network = calculate\_ic(  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 66, in calculate\_ic  
raise ValueError(“No contacts found for selection”)  
ValueError: No contacts found for selection

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [July 17, 2023, 1:39pm UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/4 "2023-07-17T13:39:38Z")

</div>

Well - it is then not a PDB structure, but a docked model.

And it looks like your chain IDs are different… I see R and P.  
Check the chainIDs in your model and use those for PRODIGY

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<div class="post-metadata">

**Author:** ![metanoia](https://avatars.discourse-cdn.com/v4/letter/m/7c8e57/32.png) [@metanoia](https://ask.bioexcel.eu/u/metanoia)\
**Post date:** [July 17, 2023, 1:47pm UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/5 "2023-07-17T13:47:32Z")

</div>

Ahhhh I see now. Those were my chain IDs. They were right next to the three letter amino acid codes in my generated docked model PDB files. Thank you so much!

I’m still new to these computational tools, 😅

My run worked now!

So I didn’t have to mind “structure contains gaps” after all

![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/8fcca7f4fabac8da57b9973e14d56c1c61d8f286.png)

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<div class="post-metadata">

**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [August 3, 2023, 8:24am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/6 "2023-08-03T08:24:31Z")

</div>

I have also the same issues after running. Can anyone resolve my issues?===========================================================================  
command: /usr/local/bin/prodigy CD19\_Hc.pdb --selection A B --temperature 25.0 --contact\_list --pymol\_selection  
exit status: 1  
log:  
[+] Reading structure file: /data/runs/oDU\_3S58Dq6t/CD19\_Hc.pdb  
[+] Parsed structure file CD19\_Hc (2 chains, 280 residues)  
Traceback (most recent call last):  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa\_tools.py”, line 207, in execute\_freesasa\_api  
struct = structureFromBioPDB(  
File “src/structure.pyx”, line 510, in freesasa.structureFromBioPDB  
File “src/structure.pyx”, line 187, in freesasa.Structure.setRadiiWithClassifier  
File “src/structure.pyx”, line 208, in freesasa.Structure.setRadii  
AssertionError: Error: Radius array is \<= 0 for the residue: GLN ,atom: OT1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):  
File “/usr/local/bin/prodigy”, line 8, in   
sys.exit(main())  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 421, in main  
prodigy.predict(  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 161, in predict  
\_, cmplx\_sasa = execute\_freesasa\_api(self.structure)  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa\_tools.py”, line 213, in execute\_freesasa\_api  
error\_message = “” + os.linesep()  
TypeError: ‘str’ object is not callable

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 3, 2023, 9:14am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/7 "2023-08-03T09:14:31Z")

</div>

OT1 is not an official PDB naming…

Instead of OT1 and OT2 use O and OXT

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<div class="post-metadata">

**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [August 3, 2023, 11:04am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/8 "2023-08-03T11:04:53Z")

</div>

**I have replaced it as per your suggestions. But some errors came.**

# 

command: /usr/local/bin/prodigy CD19\_Hc.pdb --selection A B --temperature 25.0 --contact\_list --pymol\_selection  
exit status: 1  
log:  
[+] Reading structure file: /data/runs/oDU\_3S5c-d4M/CD19\_Hc.pdb  
[+] Parsed structure file CD19\_Hc (2 chains, 280 residues)  
Traceback (most recent call last):  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa\_tools.py”, line 207, in execute\_freesasa\_api  
struct = structureFromBioPDB(  
File “src/structure.pyx”, line 510, in freesasa.structureFromBioPDB  
File “src/structure.pyx”, line 187, in freesasa.Structure.setRadiiWithClassifier  
File “src/structure.pyx”, line 208, in freesasa.Structure.setRadii  
AssertionError: Error: Radius array is \<= 0 for the residue: ILE ,atom: CD

During handling of the above exception, another exception occurred:

Traceback (most recent call last):  
File “/usr/local/bin/prodigy”, line 8, in   
sys.exit(main())  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 421, in main  
prodigy.predict(  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 161, in predict  
\_, cmplx\_sasa = execute\_freesasa\_api(self.structure)  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa\_tools.py”, line 213, in execute\_freesasa\_api  
error\_message = “” + os.linesep()  
TypeError: ‘str’ object is not callable

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 3, 2023, 11:19am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/9 "2023-08-03T11:19:22Z")

</div>

Read the error message… The problem is CD of ILE - whose proper naming is CD1.

Sorry about all those issues, but they come from the library of freesasa and not prodigy directly.  
Again, proper standard names are important

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<div class="post-metadata">

**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [August 3, 2023, 11:33am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/10 "2023-08-03T11:33:37Z")

</div>

Thanks a lot. Now it’s working.

---

<div class="post-metadata">

**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [August 4, 2023, 5:38am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/11 "2023-08-04T05:38:38Z")

</div>

Hello Sir Can you resolve this issue?  
command: /usr/local/bin/prodigy Hc\_before\_MD.pdb --selection X XX --temperature 25.0 --contact\_list --pymol\_selection  
exit status: 1  
log:  
[+] Reading structure file: /data/runs/oDU\_3S5SlNVr/Hc\_before\_MD.pdb  
[+] Parsed structure file Hc\_before\_MD (2 chains, 280 residues)  
Traceback (most recent call last):  
File “/usr/local/bin/prodigy”, line 8, in   
sys.exit(main())  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 421, in main  
prodigy.predict(  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 154, in predict  
self.ic\_network = calculate\_ic(  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 66, in calculate\_ic  
raise ValueError(“No contacts found for selection”)  
ValueError: No contacts found for selection

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 4, 2023, 8:17am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/12 "2023-08-04T08:17:28Z")

</div>

We can not - the issue is on your side… Check carefully the chainIDs you are giving as argument.

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<div class="post-metadata">

**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [August 8, 2023, 7:35am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/13 "2023-08-08T07:35:29Z")

</div>

This issue was resolved. Thank u.

Can we check which amino acid residues are involved in the below attached

[+] No. of intermolecular contacts: 13  
[+] No. of charged-charged contacts: 0  
[+] No. of charged-polar contacts: 2  
[+] No. of charged-apolar contacts: 1  
[+] No. of polar-polar contacts: 1  
[+] No. of apolar-polar contacts: 5  
[+] No. of apolar-apolar contacts: 4  
[+] Percentage of apolar NIS residues: 42.98  
[+] Percentage of charged NIS residues: 24.68

---

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 8, 2023, 9:16am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/14 "2023-08-08T09:16:18Z")

</div>

PRODIGY should generate a file with the contact (.ic)

It is part of the output you can download from the server

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**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [August 8, 2023, 9:23am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/15 "2023-08-08T09:23:28Z")

</div>

Okay. Thank you.

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [August 10, 2023, 8:59am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/17 "2023-08-10T08:59:25Z")

</div>

> ValueError: No contacts found for selection

Check the chain you selected…. no contacts were identified.

---

<div class="post-metadata">

**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [September 9, 2024, 6:32am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/18 "2024-09-09T06:32:03Z")

</div>

Hello Sir  
I have issues with the PRODIGY error running my PDB file containing my docked proteins after a 200ns MD simulation run.

# ===========================================================================

command: prodigy trj\_200.pdb --selection C D,A,B --temperature 25.0 --contact\_list --pymol\_selection  
exit status: 1  
log:  
[+] Reading structure file: /data/runs/3X9mkkcA/trj\_200.pdb  
[!] Structure ‘trj\_200’ could not be parsed  
Traceback (most recent call last):  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/parsers.py”, line 158, in parse\_structure  
s = sparser.get\_structure(sname, path)  
File “/usr/local/lib/python3.10/site-packages/Bio/PDB/PDBParser.py”, line 100, in get\_structure  
self.\_parse(lines)  
File “/usr/local/lib/python3.10/site-packages/Bio/PDB/PDBParser.py”, line 123, in \_parse  
self.trailer = self.\_parse\_coordinates(coords\_trailer)  
File “/usr/local/lib/python3.10/site-packages/Bio/PDB/PDBParser.py”, line 198, in \_parse\_coordinates  
resseq = int(line[22:26].split()[0]) # sequence identifier  
ValueError: invalid literal for int() with base 10: ‘A’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):  
File “/usr/local/bin/prodigy”, line 8, in   
sys.exit(main())  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 414, in main  
structure, n\_chains, n\_res = parse\_structure(struct\_path)  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/parsers.py”, line 161, in parse\_structure  
raise Exception(exeption)  
Exception: invalid literal for int() with base 10: ‘A’

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [September 9, 2024, 7:10am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/19 "2024-09-09T07:10:33Z")

</div>

You might want to run your PDB file through pdb\_tidy from our pdb-tools software.  
There might be some formatting issues.

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<div class="post-metadata">

**Author:** ![AKD](https://avatars.discourse-cdn.com/v4/letter/a/e99b99/32.png) [@AKD](https://ask.bioexcel.eu/u/AKD)\
**Post date:** [December 28, 2024, 1:15pm UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/20 "2024-12-28T13:15:31Z")

</div>

Hello Sir  
I have issues with the PRODIGY error running my PDB file containing my docked proteins after a 20ns MD simulation run.

### PRODIGY\_708814

[+] Reading structure file: /data/runs/708814/trj\_20.pdb  
[+] Parsed structure file trj\_20 (4 chains, 1625 residues)  
Traceback (most recent call last):  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa\_tools.py”, line 207, in execute\_freesasa\_api  
struct = structureFromBioPDB(  
File “src/structure.pyx”, line 584, in freesasa.structureFromBioPDB  
File “src/structure.pyx”, line 214, in freesasa.Structure.setRadiiWithClassifier  
File “src/structure.pyx”, line 235, in freesasa.Structure.setRadii  
AssertionError: Error: Radius is \<= 0 (-1.0) for the residue: ILE, atom: CD

During handling of the above exception, another exception occurred:

Traceback (most recent call last):  
File “/usr/local/bin/prodigy”, line 8, in   
sys.exit(main())  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 421, in main  
prodigy.predict(  
File “/usr/local/lib/python3.10/site-packages/prodigy/predict\_IC.py”, line 161, in predict  
\_, cmplx\_sasa = execute\_freesasa\_api(self.structure)  
File “/usr/local/lib/python3.10/site-packages/prodigy/lib/freesasa\_tools.py”, line 213, in execute\_freesasa\_api  
error\_message = “” + os.linesep()  
TypeError: ‘str’ object is not callable

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [December 29, 2024, 9:24am UTC](https://ask.bioexcel.eu/t/prodigy-error-running-my-pdb-file-containing-my-docked-proteins-from-cluspro/4418/21 "2024-12-29T09:24:50Z")

</div>

Your PDB file does not have the standard PDB names:

ILE, atom: CD should be CD1

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