Protein conformational transitions calculations

Annotation:
StepAnnotation
Step 1: Pdb
origin.pdb
Manual Input
Properties Input:
1ake
Empty.
pdbe - PDB in Europe REST API
Step 2: Pdb
target.pdb
Manual Input
Properties Input:
4ake
Empty.
pdbe - PDB in Europe REST API
Step 3: ExtractChain
Output dataset 'output_pdb_path' from step 1
origin.chains.pdb
Manual Input
Properties Input:
["A"]
False
check_structure
pdb
Step 4: ExtractChain
Output dataset 'output_pdb_path' from step 2
target.chains.pdb
Manual Input
Properties Input:
["A"]
False
check_structure
pdb
Step 5: RemoveMolecules
Output dataset 'output_structure_path' from step 3
origin.chains.nolig.pdb
Manual Input
Properties Input:
[{"name": "AP5"}]
pdb
Step 6: GodmdPrep
Output dataset 'output_molecules_path' from step 5
Output dataset 'output_structure_path' from step 4
mygodmd_prep.aln
mygodmd_prep.aln
Manual Input
Properties Input:
12.0
2.0
EPAM250
water
aln
aln
Step 7: GodmdRun
Output dataset 'output_molecules_path' from step 5
Output dataset 'output_structure_path' from step 4
Output dataset 'output_aln_orig_path' from step 6
Output dataset 'output_aln_target_path' from step 6
select at runtime
origin-target.godmd.log
origin-target.godmd.ene.out
origin-target.godmd.mdcrd
origin-target.godmd.pdb
Manual Input
Properties Input:
{"temp": 400}
discrete
log
log
trj
Step 8: CpptrajConvert
Output dataset 'output_pdb_path' from step 7
Output dataset 'output_trj_path' from step 7
mycpptraj_convert.mdcrd
Manual Input
Properties Input:
1
-1
1
all-atoms - All system atoms
dcd - AMBER trajectory format
cpptraj
mdcrd