# PRODIGY

**URL:** https://ask.bioexcel.eu/c/prodigy/17.md?page=1

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**Page:** 2

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## [Prodigy Error: Radius array is \<= 0 for the residue: ILE ,atom: CD](https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375)

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**Author:** [@waldo.acevedo](https://ask.bioexcel.eu/u/waldo.acevedo)\
**Replies:** 2\
**Last updated:** [June 12, 2023, 7:05am UTC](https://ask.bioexcel.eu/t/prodigy-error-radius-array-is-0-for-the-residue-ile-atom-cd/4375 "2023-06-12T07:05:31Z")

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Please, anyone, help me to fix my run failed ( see below)? =========================================================================== command: /usr/local/bin/prodigy neuroplastin\_peptide\_c.pdb --selection A B --tempera…

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## [The run is failing with an exit code 2. There is absolutely nothing in the log so I don't know how to fix the error](https://ask.bioexcel.eu/t/the-run-is-failing-with-an-exit-code-2-there-is-absolutely-nothing-in-the-log-so-i-dont-know-how-to-fix-the-error/4262)

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**Author:** [@120115](https://ask.bioexcel.eu/u/120115)\
**Replies:** 1\
**Last updated:** [April 14, 2023, 4:45am UTC](https://ask.bioexcel.eu/t/the-run-is-failing-with-an-exit-code-2-there-is-absolutely-nothing-in-the-log-so-i-dont-know-how-to-fix-the-error/4262 "2023-04-14T04:45:40Z")

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## [PRODIGY running error](https://ask.bioexcel.eu/t/prodigy-running-error/4259)

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**Author:** [@yammy](https://ask.bioexcel.eu/u/yammy)\
**Replies:** 0\
**Last updated:** [April 13, 2023, 2:03am UTC](https://ask.bioexcel.eu/t/prodigy-running-error/4259 "2023-04-13T02:03:45Z")

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Hi, I am using the PRODIGY program to obtain dissociation constant of protein-protein complex. But, the status of the job is falied like picture… Any solution? Thank you.

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## [I get this error run pcm\_3Qt-inH9 is no longer accessible, please re-submit](https://ask.bioexcel.eu/t/i-get-this-error-run-pcm-3qt-inh9-is-no-longer-accessible-please-re-submit/4227)

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**Author:** [@LeaAraujo](https://ask.bioexcel.eu/u/LeaAraujo)\
**Replies:** 2\
**Last updated:** [March 30, 2023, 6:36am UTC](https://ask.bioexcel.eu/t/i-get-this-error-run-pcm-3qt-inh9-is-no-longer-accessible-please-re-submit/4227 "2023-03-30T06:36:02Z")

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Hello, I am being trying to summit a Protein Protein Dock complex from ClusPro to get means of the bidding energy and I get the following error: run pcm\_3Qt-inH9 is no longer accessible, please re-submit. Please help me …

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## [Comparing the binding affinity of three chains vs two chains](https://ask.bioexcel.eu/t/comparing-the-binding-affinity-of-three-chains-vs-two-chains/4221)

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**Author:** [@Franz](https://ask.bioexcel.eu/u/Franz)\
**Replies:** 1\
**Last updated:** [March 29, 2023, 8:19am UTC](https://ask.bioexcel.eu/t/comparing-the-binding-affinity-of-three-chains-vs-two-chains/4221 "2023-03-29T08:19:10Z")

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Hello, I hope this message finds you well. What is the best way to compare the binding affinity of a complex with three unique chains to a complex with two unique chains using PRODIGY? Should I run PRODIGY with each cha…

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## [Prodigy server not working](https://ask.bioexcel.eu/t/prodigy-server-not-working/4113)

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**Author:** [@GraceR](https://ask.bioexcel.eu/u/GraceR)\
**Replies:** 7\
**Last updated:** [March 28, 2023, 6:35am UTC](https://ask.bioexcel.eu/t/prodigy-server-not-working/4113 "2023-03-28T06:35:37Z")

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Hello, I’ve been trying to use the Prodigy server, however it appears to be not working properly - once I have submitted the request, it is queueing but I am not getting results (even after a full day of waiting). I don…

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## [Kd patent in prodigy](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200)

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**Author:** [@Nil](https://ask.bioexcel.eu/u/Nil)\
**Replies:** 4\
**Last updated:** [March 20, 2023, 9:59am UTC](https://ask.bioexcel.eu/t/kd-patent-in-prodigy/4200 "2023-03-20T09:59:48Z")

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Hi Everyone, after I uses prodigy analysis for protein-protein doc , Kd option is 3.9e-08, and 4.5e-08! Can you help me to know what exactly Kd measure in these process? And which of them is better ?

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## [Prodigy cannot predict binding affinities for protein-protein by GRAMM-X docking model.](https://ask.bioexcel.eu/t/prodigy-cannot-predict-binding-affinities-for-protein-protein-by-gramm-x-docking-model/4154)

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**Author:** [@Wutthipat1](https://ask.bioexcel.eu/u/Wutthipat1)\
**Replies:** 4\
**Last updated:** [March 7, 2023, 11:11am UTC](https://ask.bioexcel.eu/t/prodigy-cannot-predict-binding-affinities-for-protein-protein-by-gramm-x-docking-model/4154 "2023-03-07T11:11:34Z")

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I submitted my PDB file and got the following error. =========================================================================== command: /usr/local/bin/prodigy model.1\_1.pdb --selection A C --temperature 25.0 --contact…

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## [ValueError('No contacts found for selection')](https://ask.bioexcel.eu/t/valueerror-no-contacts-found-for-selection/4101)

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**Author:** [@Zalsheikh](https://ask.bioexcel.eu/u/Zalsheikh)\
**Replies:** 7\
**Last updated:** [February 9, 2023, 1:56pm UTC](https://ask.bioexcel.eu/t/valueerror-no-contacts-found-for-selection/4101 "2023-02-09T13:56:45Z")

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I am trying to predict binding affinity of a docked.pdb file ( ligand and receptor) through local prodigy tool, running the following command prodigy docked.pdb --selection A B The file has two chains; A that presents …

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## [I can't seem to get an output on prodigy](https://ask.bioexcel.eu/t/i-cant-seem-to-get-an-output-on-prodigy/4093)

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**Author:** [@Kritz25](https://ask.bioexcel.eu/u/Kritz25)\
**Replies:** 3\
**Last updated:** [February 7, 2023, 3:20pm UTC](https://ask.bioexcel.eu/t/i-cant-seem-to-get-an-output-on-prodigy/4093 "2023-02-07T15:20:10Z")

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Hi! I would like some help. I am trying to get the binding affinity between the CDRs of an antibody and the WHISCY active residues of an antigen. I used a ClusPro docked model as the input. I believe I submitted the job…

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## [Error: Radius array is \<= 0 for the residue: ILE ,atom: CD](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835)

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**Author:** [@lanselibai](https://ask.bioexcel.eu/u/lanselibai)\
**Replies:** 9\
**Last updated:** [February 5, 2023, 2:34pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-ile-atom-cd/2835 "2023-02-05T14:34:58Z")

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I got this error message when submitting a PDB: Running Prodigy for structure md\_0\_1\_noPBC ERROR: \[!\] Error when running freesasa: \[!\] Error: Radius array is \<= 0 for the residue: ILE ,atom: CD It seems that someone el…

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## [Prodigy training](https://ask.bioexcel.eu/t/prodigy-training/4066)

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**Author:** [@Daniel75](https://ask.bioexcel.eu/u/Daniel75)\
**Replies:** 2\
**Last updated:** [January 6, 2023, 2:11pm UTC](https://ask.bioexcel.eu/t/prodigy-training/4066 "2023-01-06T14:11:28Z")

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Hello, Is there any way to PRODIGY to calculate free energy in complex protein-protein containing phosphorilated Tyrosine ? Regards

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## [PRODIGY Result not showing](https://ask.bioexcel.eu/t/prodigy-result-not-showing/3842)

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**Author:** [@Ausinari](https://ask.bioexcel.eu/u/Ausinari)\
**Replies:** 2\
**Last updated:** [August 9, 2022, 11:28am UTC](https://ask.bioexcel.eu/t/prodigy-result-not-showing/3842 "2022-08-09T11:28:45Z")

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I used PRODIGY for ligand prediction and got the link to see the results via email. But the webpage still shows the status as running. Job ID: nmV\_3NAcU7Jk

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## [PRODIGY: Job running status](https://ask.bioexcel.eu/t/prodigy-job-running-status/3834)

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**Author:** [@bmaiti](https://ask.bioexcel.eu/u/bmaiti)\
**Replies:** 4\
**Last updated:** [August 4, 2022, 8:18am UTC](https://ask.bioexcel.eu/t/prodigy-job-running-status/3834 "2022-08-04T08:18:02Z")

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I am calculating binding affinity of protein-ligand complex. I submitted two jobs in last week and the links are in below. https://wenmr.science.uu.nl/prodigy/run/nfV\_3Nq-%2B8rB P - Run nfV\_3Nq+S36M. Still I see jobs …

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## [Predicted Interface Unknown](https://ask.bioexcel.eu/t/predicted-interface-unknown/3826)

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**Author:** [@christos-efthymiou](https://ask.bioexcel.eu/u/christos-efthymiou)\
**Replies:** 1\
**Last updated:** [July 29, 2022, 10:05am UTC](https://ask.bioexcel.eu/t/predicted-interface-unknown/3826 "2022-07-29T10:05:33Z")

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I would like to use the Prodigy-Crystal webserver to assess if certain interfaces are biological in two X-ray crystallography structures. However, after submitting various jobs on these structures assessing various inter…

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## [Gap in protein chain and atom naming error](https://ask.bioexcel.eu/t/gap-in-protein-chain-and-atom-naming-error/3825)

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**Author:** [@Gagan](https://ask.bioexcel.eu/u/Gagan)\
**Replies:** 1\
**Last updated:** [July 27, 2022, 9:12pm UTC](https://ask.bioexcel.eu/t/gap-in-protein-chain-and-atom-naming-error/3825 "2022-07-27T21:12:05Z")

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Dear PRODIGY Team and Users, I am facing the following errors on my protein-protein complex when submitted for PRODIGY analysis. One of my interacting protein has some residues missing due to which i am receiving error …

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## [Is pH or protonation states considered in Prodigy?](https://ask.bioexcel.eu/t/is-ph-or-protonation-states-considered-in-prodigy/3737)

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**Author:** [@lanselibai](https://ask.bioexcel.eu/u/lanselibai)\
**Replies:** 1\
**Last updated:** [May 27, 2022, 11:13am UTC](https://ask.bioexcel.eu/t/is-ph-or-protonation-states-considered-in-prodigy/3737 "2022-05-27T11:13:29Z")

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Can I ask if pH or protonation states can be considered to perform the Prodigy? e.g. if I supply the PDB with different hydrogens and all the same heavy atoms, would the results be different?

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## [Running PRODIGY ON Ubuntu](https://ask.bioexcel.eu/t/running-prodigy-on-ubuntu/3399)

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**Author:** [@Manaswini](https://ask.bioexcel.eu/u/Manaswini)\
**Replies:** 5\
**Last updated:** [May 10, 2022, 7:04am UTC](https://ask.bioexcel.eu/t/running-prodigy-on-ubuntu/3399 "2022-05-10T07:04:34Z")

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I am facing some issues with running Prodigy in Ubuntu. I downloaded the prodigy 2.0 zip file from the Github site and I do have Python 3 in my system. I tried following the usage instructions but I am not able to figure…

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## [Problem to recognize the .pdb file](https://ask.bioexcel.eu/t/problem-to-recognize-the-pdb-file/3677)

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**Author:** [@decrai60](https://ask.bioexcel.eu/u/decrai60)\
**Replies:** 1\
**Last updated:** [April 19, 2022, 7:56am UTC](https://ask.bioexcel.eu/t/problem-to-recognize-the-pdb-file/3677 "2022-04-19T07:56:07Z")

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Hi, I want just to derive the free energy change of protein-protein complex, by using a model obtained with the ClusPro program. After sending a .pdb or .mmmCIF file, the Prodigy program send me the following note: "Er…

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## [Contact area and possible applicaitons of proligy-lig in designing new proteins](https://ask.bioexcel.eu/t/contact-area-and-possible-applicaitons-of-proligy-lig-in-designing-new-proteins/3424)

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**Author:** [@Bioengineer](https://ask.bioexcel.eu/u/Bioengineer)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 1:25pm UTC](https://ask.bioexcel.eu/t/contact-area-and-possible-applicaitons-of-proligy-lig-in-designing-new-proteins/3424 "2022-01-21T13:25:39Z")

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I wish to use the prodigy-lig tool. In the results below, please let me know if the last digits (from left to right) represent the contact area between the atoms of binding amino acid and the ligand in the below results? …

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## [Problem with prodigy in ligand-protein](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383)

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**Author:** [@ladimafakher](https://ask.bioexcel.eu/u/ladimafakher)\
**Replies:** 7\
**Last updated:** [December 17, 2021, 2:25pm UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383 "2021-12-17T14:25:45Z")

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Hi I want to use the Prodigy web server for getting binding affinity for the protein-ligand complex. but unfortunately, I have got this error"Error during parsing the input structure: (1.pdb - Ligand LIG not found in ch…

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## [Prodigy "Protein-Protein" or "Protein-LIG" for protein-peptide complexes](https://ask.bioexcel.eu/t/prodigy-protein-protein-or-protein-lig-for-protein-peptide-complexes/3358)

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**Author:** [@sandra.romero](https://ask.bioexcel.eu/u/sandra.romero)\
**Replies:** 1\
**Last updated:** [December 6, 2021, 9:46am UTC](https://ask.bioexcel.eu/t/prodigy-protein-protein-or-protein-lig-for-protein-peptide-complexes/3358 "2021-12-06T09:46:44Z")

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Hi, I have a set of protein-peptide complexes for which I want to predict binding affinity. My questions are: Which tool should I use in the case of protein-peptide complexes (peptide \< 30aa), the one for protein-pr…

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## [PRODIGY error - "unable to submit job"](https://ask.bioexcel.eu/t/prodigy-error-unable-to-submit-job/3341)

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**Author:** [@thaileonglai](https://ask.bioexcel.eu/u/thaileonglai)\
**Replies:** 4\
**Last updated:** [November 19, 2021, 10:58am UTC](https://ask.bioexcel.eu/t/prodigy-error-unable-to-submit-job/3341 "2021-11-19T10:58:02Z")

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Hi. I was trying to use PRODIGY to predict the binding affinity and stability of the protein-peptide complex docked previously using HADDOCK 2.4. After I uploaded the docked complex to PRODIGY (Prodigy Webserver), I got…

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## [ProdigyLigand interpretation for drug potential](https://ask.bioexcel.eu/t/prodigyligand-interpretation-for-drug-potential/3202)

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**Author:** [@Syifa77](https://ask.bioexcel.eu/u/Syifa77)\
**Replies:** 2\
**Last updated:** [August 13, 2021, 9:52am UTC](https://ask.bioexcel.eu/t/prodigyligand-interpretation-for-drug-potential/3202 "2021-08-13T09:52:07Z")

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Hi, I want to ask about the interpretation of delta G in prodigy-ligand, the output there are 2 kinds of delta G, predict and score. which one is represent a binding free energy of protein-ligand? if the both of them, wh…

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## [Some problems WHEN doing PRODIGY](https://ask.bioexcel.eu/t/some-problems-when-doing-prodigy/3188)

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**Author:** [@xiaobingzi](https://ask.bioexcel.eu/u/xiaobingzi)\
**Replies:** 11\
**Last updated:** [August 13, 2021, 4:36am UTC](https://ask.bioexcel.eu/t/some-problems-when-doing-prodigy/3188 "2021-08-13T04:36:04Z")

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Radius array is \<= 0 for the residue: LEU ,atom: OC1 i also face similar problems ： SER OC1,OC2 not recognized SER 1HC1,1HC2,2HC1,2HC2 not recognized LYS OC1,OC2 not recognized LYS 1HC1,1HC2,2HC1,2HC2 not recognized …

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## [Error: Radius array is \<= 0 for the residue: ARG ,atom: O1](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-arg-atom-o1/2863)

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**Author:** [@atiqurrahamansikder](https://ask.bioexcel.eu/u/atiqurrahamansikder)\
**Replies:** 6\
**Last updated:** [August 1, 2021, 2:47pm UTC](https://ask.bioexcel.eu/t/error-radius-array-is-0-for-the-residue-arg-atom-o1/2863 "2021-08-01T14:47:50Z")

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I am facing this error while doing my job! What should I do? Running Prodigy for structure sol\_1 ERROR: \[!\] Error when running freesasa: \[!\] Error: Radius array is \<= 0 for the residue: ARG ,atom: O1

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## [Some problems in doing PRODIGY](https://ask.bioexcel.eu/t/some-problems-in-doing-prodigy/3187)

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**Author:** [@xiaobingzi](https://ask.bioexcel.eu/u/xiaobingzi)\
**Replies:** 0\
**Last updated:** [August 1, 2021, 8:12am UTC](https://ask.bioexcel.eu/t/some-problems-in-doing-prodigy/3187 "2021-08-01T08:12:54Z")

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Running Prodigy for structure 500000 ERROR: \[!\] Error when running freesasa: \[!\] Error: Radius array is \<= 0 for the residue: ILE ,atom: CD I use notepad++ change CD ILE to CD1 ILE but it shows： Error during parsing…

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## [Archive file of all the outputs (.tgz) doesn't exist](https://ask.bioexcel.eu/t/archive-file-of-all-the-outputs-tgz-doesnt-exist/2906)

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**Author:** [@tomasmartak](https://ask.bioexcel.eu/u/tomasmartak)\
**Replies:** 4\
**Last updated:** [May 6, 2021, 9:27am UTC](https://ask.bioexcel.eu/t/archive-file-of-all-the-outputs-tgz-doesnt-exist/2906 "2021-05-06T09:27:42Z")

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Hi, I’ve been submitting a number of models to PRODIGY and I noticed that for every single one of them, attempting to download the archive file of all outputs led me to a page stating: "The page you are looking for do…

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## [Invalid literal for int() with base 10: ""B""](https://ask.bioexcel.eu/t/invalid-literal-for-int-with-base-10-b/2873)

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**Author:** [@atiqurrahamansikder](https://ask.bioexcel.eu/u/atiqurrahamansikder)\
**Replies:** 0\
**Last updated:** [March 28, 2021, 2:44pm UTC](https://ask.bioexcel.eu/t/invalid-literal-for-int-with-base-10-b/2873 "2021-03-28T14:44:52Z")

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After uploading the PDB file to the prodigy server it shows this error- invalid literal for int() with base 10: ““B””

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## [PRODIGY is out of work](https://ask.bioexcel.eu/t/prodigy-is-out-of-work/2831)

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**Author:** [@mglgc](https://ask.bioexcel.eu/u/mglgc)\
**Replies:** 4\
**Last updated:** [March 1, 2021, 10:34pm UTC](https://ask.bioexcel.eu/t/prodigy-is-out-of-work/2831 "2021-03-01T22:34:24Z")

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First of all, I thank PRODIGY’s team for making it free available to the scientific community. As you already know, both the PRODIGY-LIGAND web server as well as the github repositoy are out of work since several days.…

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