# LINCS error for isopeptide bonds

**URL:** <https://gromacs.bioexcel.eu/t/lincs-error-for-isopeptide-bonds/6282>\
**Category:** User discussions\
**Tags:** forcefield, mdp-parameters, mdrun\
**Created:** [April 26, 2023, 7:16am UTC](https://gromacs.bioexcel.eu/t/lincs-error-for-isopeptide-bonds/6282 "2023-04-26T07:16:04Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![naskars](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@naskars](https://gromacs.bioexcel.eu/u/naskars)\
**Post date:** [April 26, 2023, 7:16am UTC](https://gromacs.bioexcel.eu/t/lincs-error-for-isopeptide-bonds/6282/1 "2023-04-26T07:16:05Z")

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GROMACS version: 2023  
GROMACS modification: No

Dear Gromacs user community,

I have the following problem in Gromacs.

I am studying a protein that has an isopeptide bond. I went through the previous post on this forum in order to create the isopeptide bond. The method I followed is as follows.

1. First, I placed the two proteins in a way that they do not overlap, and the residue of each protein (LYS and GLY), which will make the isopeptide bond is within the cutoff.
2. I defined the corresponding LYS and GLY residue in the **rtp, residuetypes, hdb, r2b** files, which will make the isopeptide bond. I have successfully created the bond. I employed the amber a99SB-disp for building the topology. Solvated the structure in water and added NaCl to have a molarity of 150mM.
3. Minimized the structure using SD and CG procedures.
4. Run NVT for 1 ns with restraint (1000KJ.mol-1) on the protein C-α atoms. V-rescale temperature coupling was used with an integration time step of 2fs.
5. Run 5 NPT simulations for 1 ns each, slowly reducing the restraint on the protein (1000,500,100,50,10 KJ.mol-1). Parrinello-Rahman pressure coupling was used.
6. Run production simulation in NPT without any restraint.

Now, when I start the production simulation, after a few ns, **LINCS error** occurs on the isopeptide bond. I looked into the previous Gromacs post on **LINCS error** and tried to implement what has been suggested before. Clearly, the starting structure is not an issue here. I used Gromacs 2023 latest version with GPU implementation. The surprising thing is that when I run my system using only the CPUs, the LINCS error does not appear. I thought I had built the software wrongly. Then I installed Gromacs 2022.3, and the same problem appeared in the production simulation for the GPU version.  
What could be the possible resolution? Is this a bug, or have I done something wrong?

Any help is appreciated.

Thanks,  
Supriyo Naskar

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<div class="post-metadata">

**Author:** ![naskars](https://avatars.discourse-cdn.com/v4/letter/n/59ef9b/32.png) [@naskars](https://gromacs.bioexcel.eu/u/naskars)\
**Post date:** [April 27, 2023, 7:15am UTC](https://gromacs.bioexcel.eu/t/lincs-error-for-isopeptide-bonds/6282/2 "2023-04-27T07:15:56Z")

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I forgot to mention that when I am making the isopeptide bond, it is not creating any improper dihedral for the specified bond.  
So, I manually added those impropers.  
However, I am getting the LINCS error for both with improper or without improper dihedrals after a few tens of ns.

What could be the reason?