AutoDock CrankPep or ADCP is an AutoDock docking engine specialized for docking peptides. It combines technology form the protein folding filed with an efficient representation of a rigid receptor as affinity grids to fold the peptide in the context of the energy landscape created by the receptor.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ module load AutodockCrankprep
[+] Loading AutodockCrankprep 1.0 on cn2882
[user@cn3144 ~]$ prepare_receptor
prepare_receptor4: receptor filename must be specified.
Usage: prepare_receptor4.py -r filename
Description of command...
-r receptor_filename
supported file types include pdb,mol2,pdbq,pdbqs,pdbqt, possibly pqr,cif
Optional parameters:
[-v] verbose output (default is minimal output)
[-o pdbqt_filename] (default is 'molecule_name.pdbqt')
[-A] type(s) of repairs to make:
'bonds_hydrogens': build bonds and add hydrogens
'bonds': build a single bond from each atom with no bonds to its closest neighbor
'hydrogens': add hydrogens
'checkhydrogens': add hydrogens only if there are none already
'None': do not make any repairs
(default is 'None')
[-C] preserve all input charges ie do not add new charges
(default is addition of gasteiger charges)
[-p] preserve input charges on specific atom types, eg -p Zn -p Fe
[-U] cleanup type:
'nphs': merge charges and remove non-polar hydrogens
'lps': merge charges and remove lone pairs
'waters': remove water residues
'nonstdres': remove chains composed entirely of residues of
types other than the standard 20 amino acids
'deleteAltB': remove XX@B atoms and rename XX@A atoms->XX
(default is 'nphs_lps_waters_nonstdres')
[-e] delete every nonstd residue from any chain
'True': any residue whose name is not in this list:
['CYS','ILE','SER','VAL','GLN','LYS','ASN',
'PRO','THR','PHE','ALA','HIS','GLY','ASP',
'LEU', 'ARG', 'TRP', 'GLU', 'TYR','MET',
'HID', 'HSP', 'HIE', 'HIP', 'CYX', 'CSS']
will be deleted from any chain.
NB: there are no nucleic acid residue names at all
in the list and no metals.
(default is False which means not to do this)
[-M] interactive
(default is 'automatic': outputfile is written with no further user input)
[-d dictionary_filename] file to contain receptor summary information
[-w] assign each receptor atom a unique name: newname is original name plus its index(1-based)
Create a batch input file (e.g. ADCP.sh). For example:
#!/bin/bash set -e module load AutodockCrankprep unzip ADCP_tutorial_data.zip cd ADCP_tutorial_data/3Q47 reduce 3Q47_rec.pdb > 3Q47_recH.pdb
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] ADCP.sh