Protein-glycan docking

HADDOCK
1

Hi
I have been trying to dock a protein with the pdb text file pasted below but i keep getting this message using HADDOCK 2.4.

" The following error occurred when processing one of your PDB file: Unable to generate topology for ligand CA. PRODRG did not create the required output:"

Could you help with suggestions please
Thank you

HETATM 1 C1 BGC 1 10.317 5.727 46.033 1.00 37.15 C
HETATM 2 O1 BGC 1 9.162 5.211 45.470 1.00 37.15 O
HETATM 3 C2 BGC 1 10.396 5.359 47.489 1.00 37.15 C
HETATM 4 O2 BGC 1 9.230 5.806 48.154 1.00 37.15 O
HETATM 5 C3 BGC 1 11.628 6.031 48.055 1.00 37.15 C
HETATM 6 O3 BGC 1 11.750 5.768 49.444 1.00 37.15 O
HETATM 7 C4 BGC 1 12.851 5.514 47.313 1.00 37.15 C
HETATM 8 O4 BGC 1 13.824 6.402 47.842 1.00 37.15 O
HETATM 9 C5 BGC 1 12.692 5.733 45.807 1.00 37.15 C
HETATM 10 O5 BGC 1 11.443 5.184 45.344 1.00 37.15 O
HETATM 11 C6 BGC 1 13.790 5.081 44.987 1.00 37.15 C
HETATM 12 O6 BGC 1 13.529 5.200 43.593 1.00 37.15 O
HETATM 13 C7 GLC 2 14.999 5.810 48.300 1.00 15.49 C
HETATM 14 C1A GLC 2 18.755 9.158 49.940 1.00 15.49 C
HETATM 15 C8 GLC 2 15.257 6.245 49.752 1.00 15.49 C
HETATM 16 C2A GLC 2 19.812 10.171 49.500 1.00 15.49 C
HETATM 17 O7 GLC 2 14.031 6.183 50.453 1.00 15.49 O
HETATM 18 O2A GLC 2 19.213 11.438 49.313 1.00 15.49 O
HETATM 19 C9 GLC 2 15.810 7.676 49.825 1.00 15.49 C
HETATM 20 C3B GLC 2 20.496 9.742 48.214 1.00 15.49 C
HETATM 21 O8 GLC 2 16.212 7.974 51.151 1.00 15.49 O
HETATM 22 O3A GLC 2 21.380 10.772 47.811 1.00 15.49 O
HETATM 23 C10 GLC 2 17.003 7.802 48.905 1.00 15.49 C
HETATM 24 C4A GLC 2 21.279 8.458 48.457 1.00 15.49 C
HETATM 25 N4A GLC 2 17.674 9.087 48.967 1.00 15.49 N
HETATM 26 O9 GLC 2 21.243 7.894 47.043 1.00 15.49 O
HETATM 27 C11 GLC 2 16.548 7.468 47.485 1.00 15.49 C
HETATM 28 C5A GLC 2 20.809 7.640 49.581 1.00 15.49 C
HETATM 29 O10 GLC 2 16.112 6.097 47.450 1.00 15.49 O
HETATM 30 C12 GLC 2 17.669 7.684 46.468 1.00 15.49 C
HETATM 31 C6A GLC 2 21.676 6.505 50.062 1.00 15.49 C
HETATM 32 O6A GLC 2 22.276 7.077 51.223 1.00 15.49 O
HETATM 33 C7A GLC 2 19.547 7.947 50.357 1.00 15.49 C
HETATM 34 C13 GLC 3 22.455 7.713 46.226 1.00 39.46 C
HETATM 35 C14 GLC 3 21.856 7.014 44.943 1.00 39.46 C
HETATM 36 O11 GLC 3 20.515 7.468 44.720 1.00 39.46 O
HETATM 37 C15 GLC 3 21.894 5.544 44.879 1.00 39.46 C
HETATM 38 O12 GLC 3 21.840 5.115 43.521 1.00 39.46 O
HETATM 39 C16 GLC 3 23.135 4.963 45.493 1.00 39.46 C
HETATM 40 O13 GLC 3 23.285 3.525 45.467 1.00 39.46 O
HETATM 41 C17 GLC 3 23.218 5.465 46.944 1.00 39.46 C
HETATM 42 O14 GLC 3 23.376 6.850 46.983 1.00 39.46 O
HETATM 43 C18 GLC 3 24.435 4.916 47.629 1.00 39.46 C
HETATM 44 O15 GLC 3 25.614 5.228 46.898 1.00 39.46 O
HETATM 45 C19 GLC 4 24.522 3.027 45.032 1.00 19.26 C
HETATM 46 C20 GLC 4 24.413 2.502 43.591 1.00 19.26 C
HETATM 47 O16 GLC 4 23.895 3.507 42.722 1.00 19.26 O
HETATM 48 C21 GLC 4 23.518 1.276 43.558 1.00 19.26 C
HETATM 49 O17 GLC 4 23.460 0.747 42.243 1.00 19.26 O
HETATM 50 C22 GLC 4 24.093 0.235 44.500 1.00 19.26 C
HETATM 51 O18 GLC 4 23.244 -0.903 44.507 1.00 19.26 O
HETATM 52 C23 GLC 4 24.183 0.829 45.903 1.00 19.26 C
HETATM 53 O19 GLC 4 25.015 1.999 45.872 1.00 19.26 O
HETATM 54 C24 GLC 4 24.728 -0.184 46.913 1.00 19.26 C
CONECT 1 2 10 3
CONECT 2 1
CONECT 3 1 4 5
CONECT 4 3
CONECT 5 3 6 7
CONECT 6 5
CONECT 7 5 8 9
CONECT 8 7 13
CONECT 9 7 10 11
CONECT 10 1 9
CONECT 11 9 12
CONECT 12 11
CONECT 13 8 15 29
CONECT 14 16 33 25
CONECT 15 13 19 17
CONECT 16 14 18 20
CONECT 17 15
CONECT 18 16
CONECT 19 15 21 23
CONECT 20 16 22 24
CONECT 21 19
CONECT 22 20
CONECT 23 19 25 27
CONECT 24 20 26 28
CONECT 25 23 14
CONECT 26 24 34
CONECT 27 23 29 30
CONECT 28 24 31 33
CONECT 29 13 27
CONECT 30 27
CONECT 31 28 32
CONECT 32 31
CONECT 33 14 28
CONECT 34 26 35 42
CONECT 35 34 36 37
CONECT 36 35
CONECT 37 35 38 39
CONECT 38 37
CONECT 39 37 40 41
CONECT 40 39 45
CONECT 41 39 42 43
CONECT 42 34 41
CONECT 43 41 44
CONECT 44 43
CONECT 45 40 46 53
CONECT 46 45 48 47
CONECT 47 46
CONECT 48 46 49 50
CONECT 49 48
CONECT 50 48 51 52
CONECT 51 50
CONECT 52 50 53 54
CONECT 53 45 52
CONECT 54 52
END

2

The problem does not seem to come from the PDB you pasted in your message…

Do you have heteroatom in your receptor PDB file?

Did you define the ligand as glycan (obviously it is one)?

3

All hetroatom in my receptor has been removed.

The error is coming from the glycan.
I’m not sure what the problem is…

Thank you for your prompt response

4

share your input PDBs

did you select glycan as molecules type for the glycan?

5

YES I DID SELECT GLYGAN AS THE MOLECULE TYPE.
Docking PDB:1hny and PubChem CID: 41774

PLEASE FIND ATTACHED THE PDB

image
image1920×1080 211 KB

6

no attachment here - no PDB file

7

PS: Share the exact files you are using. The protein (1hny) does contain water and some ions, one of which being the CA possibly giving the problem

8

I get this error message: “Error in PDB file. Your PDB contains multiple residues with number 2 in chain B or duplicated atom names.” when i dock with “glycan1” attached here.
I used the pdb tools “selaltloc” and i got an “output1”. After docking with output1, the glycan (output1) was broken. Please help me to rectify this problem

thank you
glycan1.pdb (15.3 KB)
[output_1
cluster1_1 (1).pdb (391.1 KB)
cluster1_2.pdb (391.1 KB)
cluster1_3.pdb (391.1 KB)
cluster1_4.pdb (391.1 KB)
.pdb|attachment](upload://pJ4Oqy7J709taIvjXihNGonefzY.pdb) (8.5 KB)

9

output_1 (4).pdb (8.5 KB)

10

G6D is not supported. Check for the list of supported saccharine units:

https://wenmr.science.uu.nl/haddock2.4/library

11

And same story for AC1

Do check the list of supported ligands, and their naming.

12

Ok thank you. i will try this now and get back here.

13

Continuing the discussion from Protein-glycan docking:

After changing the AC1 and G6D as you suggested, the broken bonds were corrected as seen in image 1.

image
image1920×1080 193 KB

However when compared to the crystal structure, (image 2), it seems the there are different interractions.

image
image928×728 133 KB

I have cross-check the composition of acarbose (Image 3) and found one of the structure is not captured in the haddock library
image
We’ve got BGC and GLC. But the remaining name AC1 and G6D are not captured in the library. Please advice on what to do
Thank you so much for constant help on this platform

14

We’ve got BGC and GLC. But the remaining name AC1 and G6D are not captured in the library. Please advice on what to do
Thank you so much for constant help on this platform

Not supported… Someone would have to create the topologies and parameters for those. This is not so trivial.

You can try to see if there are present in the ATB server:

https://atb.uq.edu.au/index.py

Or parametrise those with ATB

15

I have tried to use haddock to dock acarbose and human pancreatic amylase (1b2y) but failed.
So, could you please dock it for me while I pay for the service?
Thank you