# Non standart ligands
**URL:** https://ask.bioexcel.eu/t/non-standart-ligands/6011
**Category:** HADDOCK
**Created:** [February 24, 2026, 11:10pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011 "2026-02-24T23:10:15Z")
**Posts on this page:** 18
**Page:** 1
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [February 24, 2026, 11:10pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/1 "2026-02-24T23:10:15Z")
Greetings,
I am trying to dock a protease (213 residues) to an integrin (1,847 residues).
However, I would like to use the integrin embedded in a CHARMM-GUI lipid bilayer model composed of POPE and CHL. In this case, the integrin PDB file contains 3,137 residues/molecules.
I generated the .top and .par files for POPE and CHL using Antechamber.
Although the results change when I include them in the .cfg files, the output cluster models (cluster\_1\_model\_1.pdb) do not show the POPE and CHL molecules.
Is this correct?
This is the .cfg input.
_ **run\_dir = “resuparamAMber”** _
_ **execution mode** _
_**mode = “local”
ncores = 48**_
_ **molecules to be docked** _
_**molecules = [
“data/protein2.pdb”,
“data/protein1.pdb”
]**_
_**[topoaa]
autohis = false
ligand\_param\_fname = “data/ligandCHL\_CNS.par”
ligand\_top\_fname = “data/ligandCHL\_CNS.top”
delenph = false**_
_**[topoaa.mol1]
nhisd = 0
nhise = 1
hise\_1 = 75
[topoaa.mol2]
nhisd = 1
hisd\_1 = 76
nhise = 1
hise\_1 = 15**_
_**[rigidbody]
tolerance = 20
sampling = 100
ranair = true
ligand\_param\_fname = “data/ligandCHL\_CNS.par”
ligand\_top\_fname = “data/ligandCHL\_CNS.top”**_
_**[caprieval]**_
_**[seletop]
select = 5**_
_**[flexref]
tolerance = 50
contactairs = true
ligand\_param\_fname = “data/ligandCHL\_CNS.par”
ligand\_top\_fname = “data/ligandCHL\_CNS.top”**_
_**[caprieval]**_
_**[emref]
tolerance = 50
contactairs = true
ligand\_param\_fname = “data/pop\_CNS.par”
ligand\_top\_fname = “data/pop\_CNS.top”**_
_**[clustfcc]
min\_population = 1**_
_**[seletopclusts]
top\_models = 10**_
_**[caprieval]**_
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [February 25, 2026, 8:19am UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/2 "2026-02-25T08:19:36Z")
Are there present in the models in the e.g. emref directory?
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [February 25, 2026, 12:20pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/3 "2026-02-25T12:20:21Z")
You mean if the ligands (CHL and/or POPE) are present in the .pdb generated in the emref step? They are not either.
By the way, I am using **Haddock3**
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [February 25, 2026, 7:08pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/4 "2026-02-25T19:08:40Z")
And in the topoaa directory?
If not then someway they get filtered out…
Note that this was never tested with HADDOCK3.
Might work in the 2.4 web server though.
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [February 25, 2026, 7:31pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/5 "2026-02-25T19:31:14Z")
POPE and CHL are not in the 0\_topoaa either
Just to be totaly clear: in this approach I want to try CHL and POPE belongs to the protein (integrin) to which I want dock protein2 (protease). The problem is CHL and POPE are not difined in Haddock3.
I did try already in the server, but the integrin-membrane protein does not load. It gives this error:
_**An error has occurred, here are the details: invalid literal for int() with base 10: ‘A245’**_
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [February 26, 2026, 2:52am UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/6 "2026-02-26T02:52:48Z")
Can you share the PDB file of your membrane embedded protein?
The lipids must have the same chainID as the protein, and be defined as HETATM
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [February 26, 2026, 12:21pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/7 "2026-02-26T12:21:32Z")
It says its too big (larger than 10MB).
But here it is a part of the pdb, from the end of the protein to the first lipid bilayer molecules
ATOM 28127 HG2 LYS 1847 79.304 26.566 18.315 1.00 0.00 H
ATOM 28128 CD LYS 1847 79.944 24.499 18.137 1.00 0.00 C
ATOM 28129 HD1 LYS 1847 79.479 24.323 17.144 1.00 0.00 H
ATOM 28130 HD2 LYS 1847 79.888 23.562 18.731 1.00 0.00 H
ATOM 28131 CE LYS 1847 81.404 24.895 17.951 1.00 0.00 C
ATOM 28132 HE1 LYS 1847 81.884 25.030 18.943 1.00 0.00 H
ATOM 28133 HE2 LYS 1847 81.463 25.838 17.366 1.00 0.00 H
ATOM 28134 NZ LYS 1847 82.169 23.868 17.221 1.00 0.00 N
ATOM 28135 HZ1 LYS 1847 81.749 23.727 16.280 1.00 0.00 H
ATOM 28136 HZ2 LYS 1847 82.141 22.974 17.751 1.00 0.00 H
ATOM 28137 HZ3 LYS 1847 83.156 24.179 17.117 1.00 0.00 H
ATOM 28138 C LYS 1847 75.508 26.407 18.735 1.00 0.00 C
ATOM 28139 OT1 LYS 1847 74.484 26.536 19.458 1.00 0.00 O
ATOM 28140 OT2 LYS 1847 75.474 26.265 17.484 1.00 0.00 O
TER 28140 LYS 1847
HETATM28141 N POP 1848 21.878 3.857 19.906 1.00 0.00 N
HETATM28142 HN1 POP 1848 22.031 4.880 19.795 1.00 0.00 H
HETATM28143 HN2 POP 1848 21.310 3.747 20.770 1.00 0.00 H
HETATM28144 HN3 POP 1848 22.792 3.414 20.127 1.00 0.00 H
HETATM28145 C12 POP 1848 21.225 3.163 18.761 1.00 0.00 C
HETATM28146 H12A POP 1848 21.027 2.148 19.165 1.00 0.00 H
HETATM28147 H12B POP 1848 22.092 3.213 18.067 1.00 0.00 H
HETATM28148 C11 POP 1848 19.950 3.851 18.222 1.00 0.00 C
HETATM28149 H11A POP 1848 19.635 3.469 17.228 1.00 0.00 H
HETATM28150 H11B POP 1848 20.326 4.885 18.062 1.00 0.00 H
HETATM28151 P POP 1848 17.640 4.805 19.083 1.00 0.00 P
HETATM28152 O13 POP 1848 17.702 6.091 19.840 1.00 0.00 O
HETATM28153 O14 POP 1848 16.493 3.963 19.462 1.00 0.00 O
HETATM28154 O11 POP 1848 17.590 5.180 17.541 1.00 0.00 O
HETATM28155 O12 POP 1848 18.928 3.905 19.186 1.00 0.00 O
HETATM28156 C1 POP 1848 16.545 4.684 16.720 1.00 0.00 C
HETATM28157 HA POP 1848 15.979 5.493 16.210 1.00 0.00 H
HETATM28158 HB POP 1848 15.786 4.060 17.238 1.00 0.00 H
HETATM28159 C2 POP 1848 17.158 3.792 15.644 1.00 0.00 C
HETATM28160 HS POP 1848 17.739 2.952 16.081 1.00 0.00 H
I did also try like that
ATOM 28122 CB LYS A1847 77.717 25.239 18.939 1.00 0.00 C
ATOM 28123 HB1 LYS A1847 77.368 24.925 17.932 1.00 0.00 H
ATOM 28124 HB2 LYS A1847 77.589 24.390 19.644 1.00 0.00 H
ATOM 28125 CG LYS A1847 79.185 25.608 18.865 1.00 0.00 C
ATOM 28126 HG1 LYS A1847 79.593 25.731 19.891 1.00 0.00 H
ATOM 28127 HG2 LYS A1847 79.304 26.566 18.315 1.00 0.00 H
ATOM 28128 CD LYS A1847 79.944 24.499 18.137 1.00 0.00 C
ATOM 28129 HD1 LYS A1847 79.479 24.323 17.144 1.00 0.00 H
ATOM 28130 HD2 LYS A1847 79.888 23.562 18.731 1.00 0.00 H
ATOM 28131 CE LYS A1847 81.404 24.895 17.951 1.00 0.00 C
ATOM 28132 HE1 LYS A1847 81.884 25.030 18.943 1.00 0.00 H
ATOM 28133 HE2 LYS A1847 81.463 25.838 17.366 1.00 0.00 H
ATOM 28134 NZ LYS A1847 82.169 23.868 17.221 1.00 0.00 N
ATOM 28135 HZ1 LYS A1847 81.749 23.727 16.280 1.00 0.00 H
ATOM 28136 HZ2 LYS A1847 82.141 22.974 17.751 1.00 0.00 H
ATOM 28137 HZ3 LYS A1847 83.156 24.179 17.117 1.00 0.00 H
ATOM 28138 C LYS A1847 75.508 26.407 18.735 1.00 0.00 C
ATOM 28139 OT1 LYS A1847 74.484 26.536 19.458 1.00 0.00 O
ATOM 28140 OT2 LYS A1847 75.474 26.265 17.484 1.00 0.00 O
TER 28140 LYS 1847
HETATM28141 N POP A1848 21.878 3.857 19.906 1.00 0.00 N
HETATM28142 HN1 POP A1848 22.031 4.880 19.795 1.00 0.00 H
HETATM28143 HN2 POP A1848 21.310 3.747 20.770 1.00 0.00 H
HETATM28144 HN3 POP A1848 22.792 3.414 20.127 1.00 0.00 H
HETATM28145 C12 POP A1848 21.225 3.163 18.761 1.00 0.00 C
HETATM28146 H12A POP A1848 21.027 2.148 19.165 1.00 0.00 H
HETATM28147 H12B POP A1848 22.092 3.213 18.067 1.00 0.00 H
HETATM28148 C11 POP A1848 19.950 3.851 18.222 1.00 0.00 C
HETATM28149 H11A POP A1848 19.635 3.469 17.228 1.00 0.00 H
HETATM28150 H11B POP A1848 20.326 4.885 18.062 1.00 0.00 H
HETATM28151 P POP A1848 17.640 4.805 19.083 1.00 0.00 P
HETATM28152 O13 POP A1848 17.702 6.091 19.840 1.00 0.00 O
HETATM28153 O14 POP A1848 16.493 3.963 19.462 1.00 0.00 O
HETATM28154 O11 POP A1848 17.590 5.180 17.541 1.00 0.00 O
HETATM28155 O12 POP A1848 18.928 3.905 19.186 1.00 0.00 O
HETATM28156 C1 POP A1848 16.545 4.684 16.720 1.00 0.00 C
HETATM28157 HA POP A1848 15.979 5.493 16.210 1.00 0.00 H
HETATM28158 HB POP A1848 15.786 4.060 17.238 1.00 0.00 H
HETATM28159 C2 POP A1848 17.158 3.792 15.644 1.00 0.00 C
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [February 26, 2026, 3:42pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/8 "2026-02-26T15:42:49Z")
For HADDOCK3 it must have a valid chainID.
We can’t debug without all data and your workflow.
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [February 26, 2026, 5:29pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/9 "2026-02-26T17:29:23Z")
[protein2.pdb](https://ask.bioexcel.eu/uploads/short-url/vlpeT4ObWyApPCTaZcsR6ZzOxdD.pdb) (128.2 KB) (this is the protease, which seems to not shown any problem)
[oooooo.pdb](https://ask.bioexcel.eu/uploads/short-url/zsnwzOEGEPbPztXQdGcqk732go4.pdb) (7.5 MB) (this is the integrin embebed in the lipid bilayer - this is a truncated version, monolayer, so it fits in the 10 MB limit of this website)
[ligandCHL\_CNSpar.txt](https://ask.bioexcel.eu/uploads/short-url/4qjXwA8qmEhdhP4uJCcZjUzdX3K.txt) (4.3 KB) (par parameters for CHL ligand from antechamber)
[ligandCHL\_CNStop.txt](https://ask.bioexcel.eu/uploads/short-url/eyuuG2g2wm1MEkrV3tMNvMvjjeb.txt) (17.3 KB) (top parameters for CHL from antechamber)
It does not load the integrin-lipidibilayer in the server either, as said previously it renders the error _**An error has occurred, here are the details: invalid literal for int() with base 10: ‘A245’**_
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [March 3, 2026, 11:56am UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/10 "2026-03-03T11:56:47Z")
Hi there
I tested a simple workflow in HADDOCK3 using your input data
````auto
```
# ====================================================================
# Protein-ligand docking example
# directory in which the scoring will be done
run_dir = "run1-test"
# execution mode
mode = "local"
ncores = 40
# molecules to be docked
molecules = [
"oooooo.pdb",
"protein2.pdb"
]
# ====================================================================
# Parameters for each stage are defined below
# ====================================================================
[topoaa]
autohis = true
ligand_param_fname = "ligandCHL_CNS.par"
ligand_top_fname = "ligandCHL_CNS.top"
delenph = true
[emref]
tolerance = 20
ligand_param_fname = "ligandCHL_CNS.par"
ligand_top_fname = "ligandCHL_CNS.top"
[caprieval]
# ====================================================================
````
It does work fine and the cholesterol is still there. The `flexref` module will however most likely fail for the full membrane because of some limits. We are working on addressing things for explicit membranes.
Note that `topoaa` returns a warning about the ooooo structure (probably issues with your model…):
```auto
(haddock3) [abonvin@goodwine]: 0_topoaa > more oooooo_haddock.warn
WARNING: the bonded energy is very high:
Ebonded-total=1.971904E+06 Ebond=389658 Eangl=1.363351E+06 Eimpr=218896
Something is possibly wrong with your input structure
```
[emref\_1.pdb](https://ask.bioexcel.eu/uploads/short-url/8ZZmLBT5y9EZ2REyabdGIjoFECF.pdb) (1.9 MB)
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [March 21, 2026, 7:20pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/11 "2026-03-21T19:20:40Z")
Thanks for that. It worked. I managed to insert two components of the membrane (CHL and POPE).
It it indeed crashed in the flexreaf step. The limitations you refer are due to the size, which means a small number of atoms in the membrane could make it works?
[2026-03-20 23:19:31,652 libparallel INFO] Using 5 cores
[2026-03-20 23:23:47,698 libparallel INFO] 5 tasks finished
[2026-03-20 23:23:47,718 **init** INFO] [flexref] CNS jobs have finished
[2026-03-20 23:23:47,722 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 50.00%.
Traceback (most recent call last):
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/libs/libutil.py”, line 382, in log\_error\_and\_exit
yield
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/clis/cli.py”, line 193, in main
workflow.run()
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/libs/libworkflow.py”, line 43, in run
step.execute()
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/libs/libworkflow.py”, line 173, in execute
self.module.run() # type: ignore
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/modules/base\_cns\_module.py”, line 61, in run
self.\_run()
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/modules/refinement/flexref/ **init**.py”, line 159, in \_run
self.export\_io\_models(faulty\_tolerance=self.params[“tolerance”])
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/modules/ **init**.py”, line 310, in export\_io\_models
self.finish\_with\_error(\_msg)
File “/home/lovelace/proj/proj758/egil/haddock3/.haddock3-env/lib/python3.10/site-packages/haddock/modules/ **init**.py”, line 318, in finish\_with\_error
raise RuntimeError(reason)
RuntimeError: 100.00% of output was not generated for this module and tolerance was set to 50.00%.
[2026-03-20 23:23:47,941 libutil ERROR] 100.00% of output was not generated for this module and tolerance was set to 50.00%.
[2026-03-20 23:23:47,942 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
[2026-03-20 23:23:47,942 libutil INFO] Finished at 20/03/2026 23:23:47. For any help contact us at [GitHub · Where software is built](https://github.com/haddocking/haddock3/issues) . Tchau! 再见
! Até logo!.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [March 23, 2026, 3:44pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/12 "2026-03-23T15:44:12Z")
Dear Egil
I have been working on a membrane branch of HADDOCK3 that addresses some of the issues.
Could you share any lipid topologies/parameter files you might have to incorporate those into that version?
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [March 23, 2026, 5:16pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/13 "2026-03-23T17:16:13Z")
Dear Bovin,
Besides the CHL, which I already attached some posts above, here is the ones of POPE. I have no one else, but I could calculate them, if needed.
Also generated by antechamber.
[ligandPOPE\_CNSpar.txt](https://ask.bioexcel.eu/uploads/short-url/j9fyR8ZdxtPfx38QKuLfKWAcLL3.txt) (8.3 KB)
[ligandPOPE\_CNStop.txt](https://ask.bioexcel.eu/uploads/short-url/qEkwC1qvxYTcPSE8etiWPBf13JT.txt) (24.7 KB)
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [March 23, 2026, 5:30pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/14 "2026-03-23T17:30:27Z")
Thanks - will add those and let you know when you can test the membrane branch.
And if you want to provide more lipids, feel free to do it 🙂
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [March 30, 2026, 11:34pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/15 "2026-03-30T23:34:51Z")
OK I am going to work on them.
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [March 30, 2026, 11:40pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/16 "2026-03-30T23:40:17Z")
I was also wondering whether it makes sense to consider all residues in the _ambig.tbl_ file except those where the the lipid bilayer is inserted.
I confess
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [March 31, 2026, 5:55am UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/17 "2026-03-31T05:55:37Z")
If you have no info, defining as passive then the solvent exposed regions would make sense (i.e. filtering out all the membrane region)
---
### Author:  [@egil](https://ask.bioexcel.eu/u/egil)
#### Post date: [April 9, 2026, 2:15pm UTC](https://ask.bioexcel.eu/t/non-standart-ligands/6011/18 "2026-04-09T14:15:09Z")
Dear Bovin ,
Here are some lipids else.
Ergosterol (ERG), PAPS, POPS, POPI
[ligandERG\_CNS.par.txt](https://ask.bioexcel.eu/uploads/short-url/cL9KNBfVeYfSFcILokXzldOUFhD.txt) (5.3 KB)
[ligandERG\_CNS.top.txt](https://ask.bioexcel.eu/uploads/short-url/9pdZBtRxYGbGJUTCSkA0QPC3gb9.txt) (16.8 KB)
[ligandPAPS\_CNS.par.txt](https://ask.bioexcel.eu/uploads/short-url/dxDnlJt20ep9N6mzsi5Yu4VsopE.txt) (8.1 KB)
[ligandPAPS\_CNS.top.txt](https://ask.bioexcel.eu/uploads/short-url/5XQuqvb151NCcz9bMAD2fLVZ9uU.txt) (25.9 KB)
[ligandPOPS\_CNS.par.txt](https://ask.bioexcel.eu/uploads/short-url/yeXXqu7qMZB5imGmPNEty3vHBVe.txt) (8.0 KB)
[ligandPOPS\_CNS.top.txt](https://ask.bioexcel.eu/uploads/short-url/mlXfNLSOqRMm0iEX5nIaxmVwPn3.txt) (25.3 KB)
[POPI\_CNS.par.txt](https://ask.bioexcel.eu/uploads/short-url/s8pjd98YLNOwboKHXm7eqb1xuo5.txt) (7.6 KB)
[POPI\_CNS.top.txt](https://ask.bioexcel.eu/uploads/short-url/hiWX0uQH2KpixGhSv5Xw5EHpLKT.txt) (23.6 KB)