# Docking with a FlavoProtein

**URL:** <https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685>\
**Category:** HADDOCK\
**Created:** [November 20, 2023, 9:47am UTC](https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685 "2023-11-20T09:47:10Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![bfonseca](https://avatars.discourse-cdn.com/v4/letter/b/87869e/32.png) [@bfonseca](https://ask.bioexcel.eu/u/bfonseca)\
**Post date:** [November 20, 2023, 9:47am UTC](https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685/1 "2023-11-20T09:47:10Z")

</div>

I am trying to use HADDOCK to dock a Ligand (NADH) with a protein that contains a FAD cofactor, but when I submit the job the run always fails. Is there a way for this program to recognize the FAD as a protein cofactor?  
Thanks in advance

---

<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:** [November 20, 2023, 10:03am UTC](https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685/2 "2023-11-20T10:03:36Z")

</div>

Should work in principle - your FAD should be defined as HETATM.

The question is why is your run failing. Please share a link to your result page

---

<div class="post-metadata">

**Author:** ![bfonseca](https://avatars.discourse-cdn.com/v4/letter/b/87869e/32.png) [@bfonseca](https://ask.bioexcel.eu/u/bfonseca)\
**Post date:** [November 20, 2023, 10:19am UTC](https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685/3 "2023-11-20T10:19:50Z")

</div>

This is the link  
[https://wenmr.science.uu.nl/haddock2.4/run/3778211238/294591-SIPv3\_NADHv2](https://wenmr.science.uu.nl/haddock2.4/run/3778211238/294591-SIPv3_NADHv2)

---

<div class="post-metadata">

**Author:** ![bfonseca](https://avatars.discourse-cdn.com/v4/letter/b/87869e/32.png) [@bfonseca](https://ask.bioexcel.eu/u/bfonseca)\
**Post date:** [November 20, 2023, 11:10am UTC](https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685/4 "2023-11-20T11:10:21Z")

</div>

[https://wenmr.science.uu.nl/haddock2.4/run/3778211238/294935-SIP\_FAD\_NADH](https://wenmr.science.uu.nl/haddock2.4/run/3778211238/294935-SIP_FAD_NADH)

In this run I identified the cofactor as FAD. In the first run I identified it as UNL.

Thank you

---

<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:** [November 20, 2023, 12:37pm UTC](https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685/5 "2023-11-20T12:37:42Z")

</div>

Deleting all hydrogens from your FAD prior to submission makes it work. But then you get the next error that no restraints were defined…

---

<div class="post-metadata">

**Author:** ![bfonseca](https://avatars.discourse-cdn.com/v4/letter/b/87869e/32.png) [@bfonseca](https://ask.bioexcel.eu/u/bfonseca)\
**Post date:** [November 20, 2023, 1:37pm UTC](https://ask.bioexcel.eu/t/docking-with-a-flavoprotein/4685/6 "2023-11-20T13:37:45Z")

</div>

Thank you for the input. I will try to fix that.