Fully flexible docking using haddock3 (local)

HADDOCK
1

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
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!

2

Hi,

The second version:

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:

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?

3

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.

4

For a single residue defined as fully flexible you can’t expect much as pretty much only the side-chain will move

5

Which version of haddock3 are you using?

6

Thanks for your response. How can I make the ASN side chains as fully flexible (as they do not have continuous resids) ?

7

as you did now - but why not try first the automatic flexibility option (default)?

8

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.

9

Also, how can I define more than 20 fully flexible residues in haddock3?

10

simply define as many as needed - it should work

11

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.

12

‘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