# Issues when docking glycans **URL:** \ **Category:** HADDOCK\ **Created:** [September 19, 2023, 12:26pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536 "2023-09-19T12:26:42Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![Francesco](https://avatars.discourse-cdn.com/v4/letter/f/e47c2d/32.png) [@Francesco](https://ask.bioexcel.eu/u/Francesco)\ **Post date:** [September 19, 2023, 12:26pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/1 "2023-09-19T12:26:42Z")
Hello, I’m a webserver user of Haddock2.4 and I’m doing protein-glycan docking with glucans with mixed glycosidic linkages (beta1-3, beta1-4 and beta1-6), but, at the end of the run, beta1-6 bonds are missing. Is this a bug of the software or am I doing something wrong? here are attached: 1. the input pdb files for the protein, for one of those glucans (6-O-β-D-glucopyranosyl-D-glucose) and for the docked structure. 2. screenshots of the glucan before and after the run. thank you for your support. best Francesco [INPUT\_PROTEIN.pdb](https://ask.bioexcel.eu/uploads/short-url/iZiqqpZoqPQa5hEHKxWuPnXDncC.pdb) (344.7 KB) [6-O-β-D-glucopyranosyl-D-glucose.pdb](https://ask.bioexcel.eu/uploads/short-url/9httcbjJG46eAWvBsAcwqTpCU4G.pdb) (80.5 KB) [cluster1\_1.pdb](https://ask.bioexcel.eu/uploads/short-url/tQu6pa98JRE8W1fUfN7E1uOrCUg.pdb) (433.4 KB) ![GLUCAN_BEFORE_DOCKING](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/5623efe189ad09a6c28a1cf22222b165916813a8.png) ![GLUCAN_AFTER_DOCKING](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/1e53128369731059e47e47778353fb1968f7b145.png) ---
**Author:** ![Francesco](https://avatars.discourse-cdn.com/v4/letter/f/e47c2d/32.png) [@Francesco](https://ask.bioexcel.eu/u/Francesco)\ **Post date:** [September 20, 2023, 1:59pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/2 "2023-09-20T13:59:19Z")
Sorry to be annoying, but I need to fix this issue if possible here is the parameter file of the job if it could be helpful. [job\_params.json](https://ask.bioexcel.eu/uploads/short-url/aCoyrp3Cno5irIlXk1D5UmSgLVc.json) (440.6 KB) ---
**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:** [September 20, 2023, 3:26pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/3 "2023-09-20T15:26:56Z")
Hi Francesco It looks like that particular linkage was not implemented. Should be soon fixed… ---
**Author:** ![Francesco](https://avatars.discourse-cdn.com/v4/letter/f/e47c2d/32.png) [@Francesco](https://ask.bioexcel.eu/u/Francesco)\ **Post date:** [September 20, 2023, 3:41pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/4 "2023-09-20T15:41:36Z")
Ok thank you Alexandre for the feedback. Is it possible to receive a notification when the issue will be fixed? ---
**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:** [September 20, 2023, 5:03pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/5 "2023-09-20T17:03:24Z")
I will let you know once properly tested and implemented on the server - probably tomorrow ---
**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:** [September 21, 2023, 7:53am UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/6 "2023-09-21T07:53:09Z")
Should now be fixed. Your original json file now results in a properly connected glycan: [https://bianca.science.uu.nl/haddock2.4/result/1111111111/279341-test-glycans-1-6](https://bianca.science.uu.nl/haddock2.4/result/1111111111/279341-test-glycans-1-6) ---
**Author:** ![Francesco](https://avatars.discourse-cdn.com/v4/letter/f/e47c2d/32.png) [@Francesco](https://ask.bioexcel.eu/u/Francesco)\ **Post date:** [September 21, 2023, 2:39pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/7 "2023-09-21T14:39:25Z")
Yes, the glycan is properly connected. Thank you so much 🙏 I just need to ask for another help, always with glycans. I’ve tried to dock a molecule of 1,4-β-D-Galactobiose, but, at the end of the run, the beta1-4 bond is missing and a weird bond between the O3 and O4 is forming. I’ve compared the .psf file of this glycan with the .psf file of 1,4-β-D-Glucobiose (that is a glycan with the same number of atoms and the same connectivity as the 1,4-β-D-Galactobiose) in order to see if there were differences during the topology generation and I’ve noticed that two different chemical types are assigned for the atom number 11 (O3): ‘OH1’ for 1,4-β-D-Glucobiose and ‘OAS’ for 1,4-β-D-Galactobiose, resulting in slightly different connectivity between atoms. Maybe could be this the explanation of the issue? Here are attached: 1. the 1,4-β-D-Galactobiose input pdb file 2. the output pdb file of the the complex 3. the 1,4-β-D-Galactobiose.psf and the 1,4-β-D-Glucobiose.psf files (to see the difference that i was talking about) 4. the parameter file of the job 5. screenshots of 1,4-β-D-Galactobiose before and after the running thank you again for the help [GA4GA\_PSIMTI6.pdb](https://ask.bioexcel.eu/uploads/short-url/cWAvMb1TzDqqlrASTLBEw2ckkKF.pdb) (26.8 KB) [cluster1\_1.pdb](https://ask.bioexcel.eu/uploads/short-url/6ohnrhbzYmc43Ql61vwFkSBP9wL.pdb) (433.1 KB) [1,4-β-D-Galactobiose.psf.txt](https://ask.bioexcel.eu/uploads/short-url/w6sSWYSD19EXcVB0vfiE1rEw1ca.txt) (4.3 KB) [1,4-β-D-Glucobiose.psf.txt](https://ask.bioexcel.eu/uploads/short-url/xg7iMV66VVERMnHMJA62O1sKje3.txt) (4.3 KB) [job\_params.json](https://ask.bioexcel.eu/uploads/short-url/6Aqm3HVyhCO707vq9ZfjYZxl5G3.json) (395.5 KB) ![GLYCAN_BEFORE_DOCKING](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/3a1fe056c8ede0e029ceef1f4a9a59d188103bcb.png) ![GLYCAN_AFTER_DOCKING](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/2dd7f144649fa6d18a83b970f9311189e0cb51e6.png) ---
**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:** [September 22, 2023, 9:39am UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/8 "2023-09-22T09:39:40Z")
Seems bad luck… We use a distance cutoff to figure out the connectivity and in this case both O3 and O4 are within the distance cutoff (2.75A) of the C1 atom, which causes to patches to be applied. We can shorten this cutoff a bit (might impact the detection of other linkages in case of bad geometries). Let me run some tests first ---
**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:** [September 22, 2023, 1:24pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/9 "2023-09-22T13:24:12Z")
Ok - please try again. Should be resolved now. ---
**Author:** ![Francesco](https://avatars.discourse-cdn.com/v4/letter/f/e47c2d/32.png) [@Francesco](https://ask.bioexcel.eu/u/Francesco)\ **Post date:** [September 22, 2023, 2:54pm UTC](https://ask.bioexcel.eu/t/issues-when-docking-glycans/4536/10 "2023-09-22T14:54:12Z")
Yes it works! thank you 🙏