# Missing parameters in cyclic peptide with Gromos FF

**URL:** <https://gromacs.bioexcel.eu/t/missing-parameters-in-cyclic-peptide-with-gromos-ff/6735>\
**Category:** User discussions\
**Tags:** pdb2gmx, forcefield\
**Created:** [July 3, 2023, 8:48am UTC](https://gromacs.bioexcel.eu/t/missing-parameters-in-cyclic-peptide-with-gromos-ff/6735 "2023-07-03T08:48:52Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![fwaibl](https://avatars.discourse-cdn.com/v4/letter/f/3ec8ea/32.png) [@fwaibl](https://gromacs.bioexcel.eu/u/fwaibl)\
**Post date:** [July 3, 2023, 8:48am UTC](https://gromacs.bioexcel.eu/t/missing-parameters-in-cyclic-peptide-with-gromos-ff/6735/1 "2023-07-03T08:48:52Z")

</div>

GROMACS version: 2023.01  
GROMACS modification: No

Dear Gromacs users and developers,

I am trying to set up a system using a cyclic peptide using the Gromos forcefields. Using the gmx\_makecyclictop.pl script, everything works fine. However, I read that pdb2gmx should be able to treat cyclic peptides out-of-the-box, so I tried this approach as well. However, there seem to be missing angle and dihedral parameters in the generated topology:

```auto
[angles]
; ai aj ak funct c0 c1 c2 c3
    2 1 3 2 ga_18
    2 1 95 2 
    3 1 95 2 
   95 1 2 2 ga_32
   95 1 3 2 ga_31
    1 3 4 2 ga_13
    1 3 8 2 ga_13
    4 3 8 2 ga_13
    3 4 5 2 ga_15
    4 5 6 2 ga_15

```

```auto
[dihedrals]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
   95 1 3 4 1 
    3 1 95 82 1 
    1 3 4 5 1 gd_34
    1 3 8 10 1 gd_42
    1 3 8 10 1 gd_45
    3 4 5 6 1 gd_34
    3 8 10 12 1 gd_14
    8 10 12 14 1 gd_43
    8 10 12 14 1 gd_44
   10 12 14 16 1 gd_42

```

I assume that the bonds spanning the cycle should also have gd\_… and ga\_… parameters (those are defined in gromos54a7.ff/ffbonded.itp).

What is the recommended way to parameterize cyclic peptides for Gromacs? Should I still use the gmx\_makecyclictop.pl script? If no, can I use the topology used by pdb2gmx, or do I need to assign the missing parameters somehow? Could this be a bug in pdb2gmx?

If that helps, I can post some example files to that others can try this out. In that case, which files should I post? (it is my first post in this forum, so I don’t know how this is usually handled).

Thanks in advance for your help.

Best,  
Franz