Hi,
I am trying to run a Metadynamic simulation of the spike protein through
PLUMED 2.10.0 - AMBER24 after equilibration. I generated a pdb file from
the last .rst7 file using cpptraj:
cpptraj -p step3_input.parm7 << 'EOF'
trajin prod.rst7
autoimage
strip !.1-62706
trajout molinfo_trimer.pdb pdb
EOF
A few lines from molinfo_trimer.pdb:
CRYST1 200.369 200.369 200.369 109.47 109.47 109.47 1
ATOM 1 N MET 1 130.602 81.228 105.504 1.00 0.00
N
ATOM 2 H1 MET 1 130.656 80.281 105.850 1.00 0.00
H
ATOM 3 H2 MET 1 129.669 81.519 105.248 1.00 0.00
H
When I am running my bash script:
module purge
module load CUDA/12.8
module load AMBER/24-MPI_GPU-plumed
amber="pmemd"
${amber} -O -i metad_prod.in -p step3_input.parm7 -c prod.rst7 -o
metad_prod.out -r metad_prod.rst7 -x metad_prod.nc
Its giving bellow error:
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
!!!!! PLUMED ERROR: Only orthorhombic and truncted octahedron cells are
supported in this release.
!!!!! ABORTING RUN
Though my system has a truncated octahedron box.
Can anyone suggest what is going on? I have attached my plumed file.
Thanks
Sangita
Duke University, NC, Durham
USA
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Received on Fri Jan 23 2026 - 14:00:03 PST
