Is your ligand covalent bonded to the protein?
On Tue, Feb 6, 2024, 1:11 PM Noureen Abdelrahman via AMBER <
amber.ambermd.org> wrote:
> Hi,
>
> I am trying to run an MD simulation for a biliverdin (ligand) bound to a
> protein system, using the ff19SB force field. However, when I run my tleap
> file, I get this error message for the CM molecules in my system. Has
> anyone parameterized this molecule before?
>
> Thanks,
> Noureen
>
>
> /proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
>
> Could not find bond parameter for atom types: S - CM
>
> for atom SG at position 42.321000, -4.195000, 17.484000
>
> and atom CAC at position 42.271000, -5.667000, 18.332000.
>
> Building angle parameters.
>
>
> /proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
>
> Could not find angle parameter for atom types: S - CM - CM
>
> for atom SG at position 42.321000, -4.195000, 17.484000,
>
> atom CAC at position 42.271000, -5.667000, 18.332000,
>
> and atom CBC at position 42.998000, -6.719000, 17.994000.
>
>
> /proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
>
> Could not find angle parameter for atom types: S - CM - CT
>
> for atom SG at position 42.321000, -4.195000, 17.484000,
>
> atom CAC at position 42.271000, -5.667000, 18.332000,
>
> and atom C3C at position 41.383000, -5.509000, 19.575000.
>
>
> /proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
>
> Could not find angle parameter for atom types: 2C - S - CM
>
> for atom CB at position 40.786000, -3.743000, 16.703000,
>
> atom SG at position 42.321000, -4.195000, 17.484000,
>
> and atom CAC at position 42.271000, -5.667000, 18.332000.
>
> Building proper torsion parameters.
>
>
> /proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
>
> ** No torsion terms for atom types: 2C-S-CM-CM
>
> for atom CB at position 40.786000, -3.743000, 16.703000,
>
> atom SG at position 42.321000, -4.195000, 17.484000,
>
> atom CAC at position 42.271000, -5.667000, 18.332000,
>
> and atom CBC at position 42.998000, -6.719000, 17.994000.
>
>
> /proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Error!
>
> ** No torsion terms for atom types: 2C-S-CM-CT
>
> for atom CB at position 40.786000, -3.743000, 16.703000,
>
> atom SG at position 42.321000, -4.195000, 17.484000,
>
> atom CAC at position 42.271000, -5.667000, 18.332000,
>
> and atom C3C at position 41.383000, -5.509000, 19.575000.
>
> Building improper torsion parameters.
>
> old PREP-specified impropers:
>
> <JRA 148>: CBC C3C CAC -M
>
> <JRA 148>: CAC H28 CBC H29
>
> <JRA 148>: C2C NC C1C OC
>
> <JRA 148>: C1C C4C NC H20
>
> <JRA 148>: CHD C3C C4C NC
>
> <JRA 148>: C1D C4C CHD H30
>
> <JRA 148>: C2D CHD C1D ND
>
> <JRA 148>: C3D CHA C4D ND
>
> <JRA 148>: C4D C1A CHA H1
>
> <JRA 148>: C2A CHA C1A NA
>
> <JRA 148>: C1A C4A NA H3
>
> <JRA 148>: C3A CHB C4A NA
>
> <JRA 148>: C2A C4A C3A CMA
>
> <JRA 148>: C3A C1A C2A CAA
>
> <JRA 148>: CBA O1A CGA O2A
>
> <JRA 148>: C4A C1B CHB H12
>
> <JRA 148>: C2B CHB C1B NB
>
> <JRA 148>: C4B C1B NB H2
>
> <JRA 148>: C3B NB C4B OB
>
> <JRA 148>: C2B C4B C3B CAB
>
> <JRA 148>: C3B C1B C2B CMB
>
> <JRA 148>: C3B CBB CAB H17
>
> <JRA 148>: CAB H18 CBB H19
>
> <JRA 148>: C2D C4D C3D CAD
>
> <JRA 148>: C3D C1D C2D CMD
>
> <JRA 148>: CBD O2D CGD O1D
>
> total 526 improper torsions applied
>
> 26 improper torsions in old prep form
>
> Building H-Bond parameters.
>
> Incorporating Non-Bonded adjustments.
>
>
> /proj/pierilab/software/amber/cuda12.2_version/amber22/bin/teLeap: Warning!
>
> Parameter file was not saved.
>
> Quit
>
>
> Exiting LEaP: Errors = 6; Warnings = 2; Notes = 1.
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Received on Tue Feb 06 2024 - 11:00:02 PST
