This has been discussed on the list before and lots of helpful suggestions
are in the archive (search for cyclic peptides).
For example, use clearpdbresmap
http://archive.ambermd.org/202009/0070.html
On Thu, Feb 17, 2022, 5:19 AM <saranya.cbmm.lodz.pl> wrote:
> Hi,
>
> I am performing the MD simulation for cyclic 22-residue peptide using
> ABMER 20. Initially the structure was minimized for 100ns by using
> Gromacs-2021. The conformer structure of the cyclic peptide contains a
> bond between N and C terminus. While I’m using the conformer structure
> to generate the parameter files for the amber simulation by using xleap
> interface the bond was missing because the amber automatically added the
> hydrogen at the N and C terminals. So I'm using the command "bond
> prot.1.N prot.22.C" to manually draw the bond between the terminals, but
> when I try to save the settings, I get the following error.
>
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
>
> Error: Could not find bond parameter for: N3 - C
> Building angle parameters.
>
> Error: Could not find angle parameter: CX - N3 - C
>
> Error: Could not find angle parameter: H - N3 - C
>
> Error: Could not find angle parameter: N3 - C - CX
>
> Error: Could not find angle parameter: N3 - C - O2
> Building proper torsion parameters.
>
> Error: ** No torsion terms for CX-N3-C-CX
>
> Error: ** No torsion terms for CX-N3-C-O2
>
> Error: ** No torsion terms for H-N3-C-CX
>
> Error: ** No torsion terms for H-N3-C-O2
> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for CX-O2-C-N3
> atoms are: CA O C N
> total 65 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
> Warning: Parameter file was not saved.
>
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Received on Thu Feb 17 2022 - 03:30:02 PST
