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 - 02:30:03 PST
