# Fully flexible docking using haddock3 (local) **URL:** \ **Category:** HADDOCK\ **Tags:** haddock\ **Created:** [June 19, 2025, 5:51pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755 "2025-06-19T17:51:21Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![biogly](https://avatars.discourse-cdn.com/v4/letter/b/c89c15/32.png) [@biogly](https://ask.bioexcel.eu/u/biogly)\ **Post date:** [June 19, 2025, 5:51pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/1 "2025-06-19T17:51:21Z")
Hi, I am trying to make the glycans attached to my protein as fully flexible. Below is how I define one of them in my .cfg file, [flexref] tolerance = 20 ambig\_fname = “ambig.tbl” unambig\_fname = “unambig.tbl” fle\_seg\_1 = “A” fle\_sta\_1 = 1864 fle\_end\_1 = 1875 I am using the info given at [Flexibility - HADDOCK3 User Manual](https://www.bonvinlab.org/haddock3-user-manual/flexibility.html#semi-flexible-segment) I also tries using it as fle\_seg\_1 = “A” seg\_sta\_1\_1 = 1867 seg\_end\_1\_1 = 1874 But i keep getting the same error, haddock.core.exceptions.ConfigurationError: The parameter block ‘fle\_\*\_1’ is not a valid expandable parameter. Any help or suggestion is greatly appreciated, thank you! ---
**Author:** ![AKravchenko](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/akravchenko/32/1168_2.png) [@AKravchenko](https://ask.bioexcel.eu/u/AKravchenko)\ **Post date:** [June 19, 2025, 7:00pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/2 "2025-06-19T19:00:08Z")
Hi, The second version: ```auto fle_seg_1 = “A” seg_sta_1_1 = 1867 seg_end_1_1 = 1874 ``` is indeed should not work for haddock3 But the first one: ```auto fle_seg_1 = “A” fle_sta_1 = 1864 fle_end_1 = 1875 ``` looks correct and parameter names are functional with the latest haddock3 release. May-be the issue is with the input pdbs, can you share those, please? ---
**Author:** ![biogly](https://avatars.discourse-cdn.com/v4/letter/b/c89c15/32.png) [@biogly](https://ask.bioexcel.eu/u/biogly)\ **Post date:** [June 19, 2025, 9:01pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/3 "2025-06-19T21:01:15Z")
Hi, Apparently, the latter parameters too don’t work with haddock, I checked the param.cfg generated at the flexref stage and it looks different. Below is what I am using which seems to work fine, nfle1 = 1 fle\_sta\_1\_1 = 1867 fle\_end\_1\_1 = 1874 On a separate note, how can i define a single residue e.g., only ASN residues to be fully flexible. When I use the following, they don’t seem to be flexible, nfle2=1 fle\_sta\_2\_1 = 58 fle\_end\_2\_1 = 58 Thanks. ---
**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:** [June 20, 2025, 6:46am UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/4 "2025-06-20T06:46:09Z")
For a single residue defined as fully flexible you can’t expect much as pretty much only the side-chain will move ---
**Author:** ![AKravchenko](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/akravchenko/32/1168_2.png) [@AKravchenko](https://ask.bioexcel.eu/u/AKravchenko)\ **Post date:** [June 20, 2025, 7:07am UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/5 "2025-06-20T07:07:14Z")
Which version of haddock3 are you using? ---
**Author:** ![biogly](https://avatars.discourse-cdn.com/v4/letter/b/c89c15/32.png) [@biogly](https://ask.bioexcel.eu/u/biogly)\ **Post date:** [June 20, 2025, 10:06pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/6 "2025-06-20T22:06:47Z")
Thanks for your response. How can I make the ASN side chains as fully flexible (as they do not have continuous resids) ? ---
**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:** [June 21, 2025, 6:30am UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/7 "2025-06-21T06:30:23Z")
as you did now - but why not try first the automatic flexibility option (default)? ---
**Author:** ![biogly](https://avatars.discourse-cdn.com/v4/letter/b/c89c15/32.png) [@biogly](https://ask.bioexcel.eu/u/biogly)\ **Post date:** [June 21, 2025, 8:24am UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/8 "2025-06-21T08:24:30Z")
I tried both automatic (defualt) and semi-flexible settings. However, the ASN residues don’t seem to be flexible in either when compared among the top scored structures. ---
**Author:** ![biogly](https://avatars.discourse-cdn.com/v4/letter/b/c89c15/32.png) [@biogly](https://ask.bioexcel.eu/u/biogly)\ **Post date:** [June 23, 2025, 4:05pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/9 "2025-06-23T16:05:01Z")
Also, how can I define more than 20 fully flexible residues in haddock3? ---
**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:** [June 23, 2025, 4:18pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/10 "2025-06-23T16:18:33Z")
simply define as many as needed - it should work ---
**Author:** ![biogly](https://avatars.discourse-cdn.com/v4/letter/b/c89c15/32.png) [@biogly](https://ask.bioexcel.eu/u/biogly)\ **Post date:** [June 23, 2025, 4:20pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/11 "2025-06-23T16:20:39Z")
This is what I get when I define the 21st residue, [2025-06-24 00:49:09,717 libutil ERROR] The parameter block ‘fle21\__1_’ is not a valid expandable parameter. ---
**Author:** ![biogly](https://avatars.discourse-cdn.com/v4/letter/b/c89c15/32.png) [@biogly](https://ask.bioexcel.eu/u/biogly)\ **Post date:** [June 23, 2025, 4:22pm UTC](https://ask.bioexcel.eu/t/fully-flexible-docking-using-haddock3-local/5755/12 "2025-06-23T16:22:16Z")
‘fle21\__1_’ somehow wasn’t pasted correctly. snippet from my .cfg input file, nfle21 = 1 fle\_sta\_21\_1 = 1950 fle\_end\_21\_1 = 1956