# PRODIGY **URL:** https://ask.bioexcel.eu/c/prodigy/17.md?page=2 [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) **Page:** 3 --- ## [Error during parsing(Unsupported non-standard amino acid found: NAG )](https://ask.bioexcel.eu/t/error-during-parsing-unsupported-non-standard-amino-acid-found-nag/2423)
**Author:** [@Kashaf](https://ask.bioexcel.eu/u/Kashaf)\ **Replies:** 1\ **Last updated:** [September 1, 2020, 5:45pm UTC](https://ask.bioexcel.eu/t/error-during-parsing-unsupported-non-standard-amino-acid-found-nag/2423 "2020-09-01T17:45:00Z")
Hello there! I receive this error while trying to perform prodigy protein-protein on top pose structure obtained from HADDOCK. What should I do to remove this error?any recommendations for online servers that remove su… --- ## [Prodigy del G and Kd values after Molecular Dynamics](https://ask.bioexcel.eu/t/prodigy-del-g-and-kd-values-after-molecular-dynamics/2339)
**Author:** [@amartya](https://ask.bioexcel.eu/u/amartya)\ **Replies:** 1\ **Last updated:** [July 17, 2020, 4:03pm UTC](https://ask.bioexcel.eu/t/prodigy-del-g-and-kd-values-after-molecular-dynamics/2339 "2020-07-17T16:03:44Z")
Hello, I was wondering how does del G and Kd values for a protein-protein complex change after simulating the complex. How comparable is Prodigy with MM-PBSA and MM-GBSA analysis of the same simulated complex? --- ## [Validity of Comparing Binding Energies for a Series of Mutations in a Native Peptide](https://ask.bioexcel.eu/t/validity-of-comparing-binding-energies-for-a-series-of-mutations-in-a-native-peptide/2277)
**Author:** [@nyyount](https://ask.bioexcel.eu/u/nyyount)\ **Replies:** 3\ **Last updated:** [July 1, 2020, 10:54am UTC](https://ask.bioexcel.eu/t/validity-of-comparing-binding-energies-for-a-series-of-mutations-in-a-native-peptide/2277 "2020-07-01T10:54:20Z")
Hi, I’m wondering whether it’s valid to compare the Prodigy binding energies and dissociation constants, for a series of peptide ligands where one amino acid is altered in each subsequent protein (peptide 1 - native; pe… --- ## [Prodigy Error Rename File?](https://ask.bioexcel.eu/t/prodigy-error-rename-file/2248)
**Author:** [@nyyount](https://ask.bioexcel.eu/u/nyyount)\ **Replies:** 2\ **Last updated:** [June 23, 2020, 6:58pm UTC](https://ask.bioexcel.eu/t/prodigy-error-rename-file/2248 "2020-06-23T18:58:42Z")
Hi, I’m using Prodigy to estimate the binding energy for a number of my docked Haddock complexes. It provides beautiful data for some complexes, but for others, the program seems to change my file name, and consistentl… --- ## [Local PRODIGY installation trouble](https://ask.bioexcel.eu/t/local-prodigy-installation-trouble/1145)
**Author:** [@melk](https://ask.bioexcel.eu/u/melk)\ **Replies:** 6\ **Last updated:** [April 2, 2020, 11:14pm UTC](https://ask.bioexcel.eu/t/local-prodigy-installation-trouble/1145 "2020-04-02T23:14:54Z")
Hello, I was just trying to get a local PRODIGY install running, and although I think I have everything in place (I cloned the PRODIGY git repository and followed the instructions in the readme to install everything els… --- ## [DNA ligand Complex](https://ask.bioexcel.eu/t/dna-ligand-complex/1802)
**Author:** [@attaribinm](https://ask.bioexcel.eu/u/attaribinm)\ **Replies:** 5\ **Last updated:** [January 22, 2020, 7:52am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802 "2020-01-22T07:52:11Z")
Hi I want to calculate the binding affinity of dsDNA ligand complex. Which interface of prodigy web server should i use i.e prodigy, prodigy protein ligand or prodigy crystal? --- ## [Error during run on Prodigy server](https://ask.bioexcel.eu/t/error-during-run-on-prodigy-server/1287)
**Author:** [@DanaNew](https://ask.bioexcel.eu/u/DanaNew)\ **Replies:** 4\ **Last updated:** [November 22, 2018, 4:42pm UTC](https://ask.bioexcel.eu/t/error-during-run-on-prodigy-server/1287 "2018-11-22T16:42:28Z")
I tried to calculate protein-protein binding energy using prodigy server, but obtained this error. I read rules for pdb filed and still do not understand what am I doing wrong… I haven’t understood how to attach file to… --- ## [Protein-protein binding affinity error](https://ask.bioexcel.eu/t/protein-protein-binding-affinity-error/1291)
**Author:** [@anurm](https://ask.bioexcel.eu/u/anurm)\ **Replies:** 1\ **Last updated:** [November 22, 2018, 9:06am UTC](https://ask.bioexcel.eu/t/protein-protein-binding-affinity-error/1291 "2018-11-22T09:06:19Z")
Hi All, I am trying to determine the binding energy of ZDOCK docked protein complex comprising of two chains of a protein dimer with one chain containing a small molecule. My problem is that, when I calculate binding af… --- ## [PRODIGY webinar](https://ask.bioexcel.eu/t/prodigy-webinar/1549)
**Author:** [@cblau](https://ask.bioexcel.eu/u/cblau)\ **Replies:** 9\ **Last updated:** [January 13, 2017, 6:52pm UTC](https://ask.bioexcel.eu/t/prodigy-webinar/1549 "2017-01-13T18:52:34Z")
Follow-up discussion on the BioExcel PRODIGY webniar [Previous page](https://ask.bioexcel.eu/c/prodigy/17.md?page=1)