# Problem with prodigy in ligand-protein

**URL:** <https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383>\
**Category:** PRODIGY\
**Created:** [December 15, 2021, 7:32pm UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383 "2021-12-15T19:32:56Z")\
**Posts on this page:** 8\
**Page:** 1

<div class="post-metadata">

**Author:** ![ladimafakher](https://avatars.discourse-cdn.com/v4/letter/l/cc9497/32.png) [@ladimafakher](https://ask.bioexcel.eu/u/ladimafakher)\
**Post date:** [December 15, 2021, 7:32pm UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/1 "2021-12-15T19:32:56Z")

</div>

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 chain A of the input data.). I checked my pdb file but I could not find any problem and ligand has existed in chain A. what is my problem and how can I solve it? I will send my pdb file in this post.  
thanks for helping me  
[1.pdb](https://ask.bioexcel.eu/uploads/short-url/U4Ct89RfwZDgVes0V4mQu6rlUQ.pdb) (378.6 KB)

---

<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 16, 2021, 8:18am UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/2 "2021-12-16T08:18:45Z")

</div>

First of all use the ligand version of PRODIGY.

And I would try giving a different chainID to your ligand to distinguish it from your protein.

---

<div class="post-metadata">

**Author:** ![ladimafakher](https://avatars.discourse-cdn.com/v4/letter/l/cc9497/32.png) [@ladimafakher](https://ask.bioexcel.eu/u/ladimafakher)\
**Post date:** [December 16, 2021, 8:37am UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/3 "2021-12-16T08:37:54Z")

</div>

I did this but I got the same error.

---

<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 16, 2021, 8:56am UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/4 "2021-12-16T08:56:35Z")

</div>

Looking at your PDB file the atom names in the ligand are not unique. Most likely causing a problem.

---

<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 16, 2021, 4:33pm UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/5 "2021-12-16T16:33:08Z")

</div>

The problem seems to come from the lower case naming of your ligand.  
Changing `lig` to `LIG` made it work:

[https://bianca.science.uu.nl/prodigy/run/adq\_3KCETcKZ](https://bianca.science.uu.nl/prodigy/run/adq_3KCETcKZ)

---

<div class="post-metadata">

**Author:** ![ladimafakher](https://avatars.discourse-cdn.com/v4/letter/l/cc9497/32.png) [@ladimafakher](https://ask.bioexcel.eu/u/ladimafakher)\
**Post date:** [December 16, 2021, 6:06pm UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/6 "2021-12-16T18:06:24Z")

</div>

thanks for your helping me  
I changed the name of lig to LIG but I got the error again" Error during parsing the input structure: (1-3.pdb - Selected chain not present in provided structure: B)". could you please send me the PDB file which you corrected to check it with mine. thanks

---

<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 17, 2021, 9:28am UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/7 "2021-12-17T09:28:04Z")

</div>

Here is the corrected PDB I used.

[1.pdb](https://ask.bioexcel.eu/uploads/short-url/d4IzNIcEbjCGJsbgBsQFVkdWRK0.pdb) (326.8 KB)

---

<div class="post-metadata">

**Author:** ![ladimafakher](https://avatars.discourse-cdn.com/v4/letter/l/cc9497/32.png) [@ladimafakher](https://ask.bioexcel.eu/u/ladimafakher)\
**Post date:** [December 17, 2021, 2:25pm UTC](https://ask.bioexcel.eu/t/problem-with-prodigy-in-ligand-protein/3383/8 "2021-12-17T14:25:45Z")

</div>

thanks so much for paying attention to my problem