インストールの具体的手順等については https://ccportal.ims.ac.jp/node/2945 をご覧ください。
https://github.com/deepmind/alphafold
#!/bin/sh
#PBS -l select=1:ncpus=12:mpiprocs=1:ompthreads=12:jobtype=core
#PBS -l walltime=72:00:00# at least 8 cpu cores will be requested internally.
# in this sample, we employ 12 cores to get enough amount of memory.
# not sure how much is necessary/required, though.# note about available memory:
# Available memory amount is proportional to ncpus value.
# If you need more memory, please increase ncpus in the header.if [ ! -z "${PBS_O_WORKDIR}" ]; then
cd "${PBS_O_WORKDIR}"
fiAF2ROOT=/local/apl/lx/alphafold2
RUNAF2=${AF2ROOT}/run_alphafold_rccs.sh# load miniconda environment (where necessary binaries reside)
. ${AF2ROOT}/conda_init.sh# Required:
# -o [output directory]
# -f [sequence file (FASTA)]# Optional arguments:
# -a [alphafold code root]
# (default: /local/apl/lx/alphafold2/alphafold-20210819)
# /local/apl/lx/alphafold2/alphafold-20210720 can be used instead.
# -d [database root]
# (default: /local/apl/lx/alphafold2/databases-20210819)
# -t [max template date] (default: 2021-08-20)
# in the original example 2020-05-14 was used (CASP14 target case?)
# -m [model names]
# (default: model_1,model_2,model_3,model_4,model_5)
# -p [preset] (default: full_dbs)
# speed/quality control. available values are casp14, full_dbs, reduced_dbs
# -Q
# change model names to _ptm version; additional scores will be available
# in output file. plDDT score will be in B-factor column of output pdbs.
sh ${RUNAF2} \
-o ./dummy_test/ \
-f query.fasta \
-Q