# Selecting active residues for basic docking using HADDOCK2.4
**URL:** https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891
**Category:** HADDOCK
**Created:** [September 12, 2022, 3:02pm UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891 "2022-09-12T15:02:43Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@sunag\_parasu](https://ask.bioexcel.eu/u/sunag_parasu)
#### Post date: [September 12, 2022, 3:02pm UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891/1 "2022-09-12T15:02:43Z")
Hello everyone, I am trying to perform protein-protein docking using HADDOCK2.4 but one of my proteins has more than 150 active residues (amino acids) and therefore isn’t being submitted. Please tell me what can I do to only select the most active residues for docking.
Thank you
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 14, 2022, 2:06pm UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891/2 "2022-09-14T14:06:14Z")
Did you filter for solvent accessibility?
If you do have active on the other protein, you could consider defining the first protein only as passive (computationally less demanding).
---
### Author:  [@sunag\_parasu](https://ask.bioexcel.eu/u/sunag_parasu)
#### Post date: [September 15, 2022, 7:53am UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891/3 "2022-09-15T07:53:43Z")
Dear professor, thank you for your reply
I chose the default option for solvent accessibility. i.e., 15.0. Should I increase this value?
For context, my first protein is an artificial protein designed in silico with nearly 530/560 amino acids as active residues and my second protein is a toll-like receptor protein.
If I choose to define my first protein as passive, could that be considered as blind docking?
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 15, 2022, 8:06am UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891/4 "2022-09-15T08:06:59Z")
If you want to do blind docking don’t use the active residue definition!!!
Use rather center of mass restraints
Check our best practice guide, e.g.: [How to use information about interactions in HADDOCK? – Bonvin Lab](https://www.bonvinlab.org/software/bpg/restraints/#2--information-about-the-interface-is-not-available)
---
### Author:  [@sunag\_parasu](https://ask.bioexcel.eu/u/sunag_parasu)
#### Post date: [September 15, 2022, 11:45am UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891/5 "2022-09-15T11:45:14Z")
Thank you for your input professor. I have applied for elevated access to change docking parameters. Please grant me access to perform blind docking.
---
### Author:  [@sunag\_parasu](https://ask.bioexcel.eu/u/sunag_parasu)
#### Post date: [September 17, 2022, 7:22am UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891/6 "2022-09-17T07:22:34Z")
Hello professor,
I recently requested permission to download and run haddock2.4 locally and want to perform blind docking. I have been following [this](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#preparing-pdb-files-for-docking) tutorial but I’m confused with defining center of mass restraints. I am following the 3rd scenario of the “defining restraints for docking” section. I am not able to understand how they are defined as there is no mention of how to define them before making the antigen-antibody.tbl file.
Could you please tell me how can I define center of mass restraints locally?
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [September 17, 2022, 5:58pm UTC](https://ask.bioexcel.eu/t/selecting-active-residues-for-basic-docking-using-haddock2-4/3891/7 "2022-09-17T17:58:10Z")
Center of mass restraints can be turned on in the run.cns file by setting cmrest = true
> **[HADDOCK2.4 manual - Ambiguous Interaction Restraints (AIRs)](https://www.bonvinlab.org/software/haddock2.4/airs/#center-of-mass-restraints)**