Update inference_multimer.sh

inference_multimer.sh

@@ -2,19 +2,17 @@
 # add `--enable_workflow` to use parallel workflow for data processing
 # add `--use_precomputed_alignments [path_to_alignments]` to use precomputed msa
 
-python3 inference.py SUGP1.fasta /data/pdb_mmcif/mmcif_files \
-    --output_dir ./ \
-    --gpus 1 \
-    --use_precomputed_alignments  alignments/ \
+python3 inference.py SUGP1.fasta /alphafold/pdb_mmcif/mmcif_files \
+    --output_dir ./output \
+    --gpus 4 \
     --model_preset multimer \
-    --uniref90_database_path /data/uniref90/uniref90.fasta \
-    --mgnify_database_path /data/mgnify/mgy_clusters_2018_12.fa \
-    --pdb70_database_path /data/pdb70/pdb70 \
-    --uniclust30_database_path /data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
-    --bfd_database_path /data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
-    --uniprot_database_path /data/uniprot/uniprot_sprot.fasta \
-    --pdb_seqres_database_path /data/pdb_seqres/pdb_seqres.txt \
-    --param_path /data/params/params_model_1_multimer.npz \
+    --uniref90_database_path /alphafold/uniref90/uniref90.fasta \
+    --mgnify_database_path /alphafold/mgnify/mgy_clusters_2018_12.fa \
+    --pdb70_database_path /alphafold/pdb70/pdb70 \
+    --uniclust30_database_path /alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
+    --uniprot_database_path /alphafold/uniprot/uniprot_trembl.fasta \
+    --pdb_seqres_database_path /alphafold/pdb_seqres/pdb_seqres.txt \
+    --param_path /alphafold/params/params_model_1_multimer.npz \
     --model_name model_1_multimer \
     --jackhmmer_binary_path `which jackhmmer` \
     --hhblits_binary_path `which hhblits` \
@@ -24,6 +22,7 @@ python3 inference.py SUGP1.fasta /data/pdb_mmcif/mmcif_files \
     --inplace \
     
     
+