prepwizard Command Help
Command: $SCHRODINGER/utilities/prepwizard
usage: prepwizard [options] inputfile outputfile
Input file should be in Maestro, PDB, or mmCIF format.
Output file should be in Maestro, PDB, or mmCIF format.
Required:
in_file Input structure file (Maestro, PDB, or mmCIF)
out_file Output structure file (Maestro, PDB, or mmCIF)
Preprocess:
-nopreprocess Skip pre-processing (useful if only ProtAssign or
refinement is desired)
-reference_st_file REFERENCE_ST_FILE
File containing reference structure to align to.
-reference_pdbid REFERENCE_PDBID
PDB ID of the structure to align to.
-nobondorders Do not assign bond orders to het groups
-noccd Do not use assign bond orders and formal charges based
on matches to the the Chemical Component Dictionary.
-skip_assigned_residues
Skip assigning bond orders to residues. If CCD is
used, residues with only single order bonds are re-
assigned based on CCD entries. Otherwise bond orders
will be assigned based on geometry.
-retain_h Do not add hydrogens. Assumes structure already
contains all necessary hydrogens.
-add_missing_h Add missing hydrogen atoms to structure. Retains
existing hydrogen atoms if they exist.
-nometaltreat Do not treat metals (adding zero-order bonds, etc)
-no_disulfides Do not create bonds between proximal sulfurs.
-no_glycosylation Do not create bonds to N- and O-linked sugars.
-palmitoylation Create palmitoylation bonds even if not included in
the CONNECT records (delete hydrogens as needed)
-antibody_cdr_scheme {Chothia,Kabat,IMGT,EnhancedChothia,AHo,None}
CDR annotation scheme.
-renumber_ab_residues
Renumber antibodies residues to match the scheme
specified with the -antibody_cdr_scheme option.
-tcr_cdr_scheme {IMGT,AHo,None}
CDR annotation scheme.
-renumber_tcr_residues
Renumber TCR residues to match the scheme specified
with the -tcr_cdr_scheme option.
-annotate_gpcr Annotate GPCR segments on qualifying chains.
-no_mse Do not convert selenomethionine residues to
methionine.
-preprocess_watdist PREPROCESS_WATDIST
If specified, during preprocessing delete waters that
are further than this distance from het groups. By
default, waters are deleted during cleanup.
-fillloops Fill missing loops with Prime.
-fasta_file CUSTOM_FASTA_FILE
If filling missing loops, the custom FASTA file to
use. If not specified, the FASTA file will be
generated from the SEQRES records in the input
structure.
-fillsidechains Rebuild incomplete side chains.
-addOXT Add terminal oxygens to polypeptides
-c, -captermini Cap termini
-cap_termini_min_atoms CAP_TERMINI_MIN_ATOMS
By default, only proteins with more than 200 atoms are
capped when -captermini is specified. Use this option
to allow capping of smaller molecules.
-noepik Do not run Epik on het groups. By default Epik is run
on all het groups, and metal binding states are
considered for hets that are within 5A of metal atoms.
-epik_pH EPIK_PH Epik target pH (default: {DEFAULT_PH})
-epik_pHt EPIK_PHT Epik pH range for generated structures (default: 2.0)
-max_states MAX_STATES, -ms MAX_STATES
Maximum number of het states to generate for each
protein complex.
-noidealizehtf Do not idealize added hydrogen temperature factors.
Optimize H-bond Assignments:
-noprotassign Do not run ProtAssign
-no_samplewater Do not sample water orientation during ProtAssign.
-use_picked_epik_state
Use the Epik state picked during preprocessing in
ProtAssign optimization.
-xtal Use crystal symmetry
-nopropka Do not use PROPKA for protonation states
-propka_pH PROPKA_PH Run PROPKA at given pH value (default: 7.4)
-label_pkas Label residues with PROPKA pKas
-simplified_pH {very_low,low,neutral,high}
Sample at given pH when not using PROPKA (default:
None)
-force FORCE_LIST FORCE_LIST
Force a particular residue to adapt the specified
state. Multiple -f specifications are permitted. See
$SCHRODINGER/utilities/protassign help for more info.
-minimize_adj_h Energy minimize all adjustable hydrogens (titratable
hydrogens, water hydrogens, hydroxyls, thiols, and
ASN/GLN carboxamide hydrogens).
Minimize and Delete Waters:
-norefine Don't run a restrained minimization job
-r RMSD, -rmsd RMSD Minimization: RMSD cutoff in angstrom (default 0.3)
-fix Minimization: Fix heavy atoms (minimize hydrogens
only)
-f {S-OPLS,OPLS_2005}, -force_field {S-OPLS,OPLS_2005}
Minimization: Version of the OPLS force field to use.
Options: OPLS_2005 or S-OPLS (default OPLS_2005)
-keepfarwat Don't delete waters far from het groups
-watdist WATDIST Distance threshold for 'far' waters (default 5.0A)
-delwater_hbond_cutoff DELWATER_HBOND_CUTOFF
If specified, delete waters that do not make at least
this number of H-bonds to non-waters. By default, this
feature is disabled (default: 0).
Other:
-preserve_st_titles Preserve titles of structures. By default they are
annotated to show which structures were prepared
-use_PDB_pH If input structure has property r_pdb_PDB_EXPDTA_PH,
use that for Epik and ProtAssign/PROPKA.
-h, --help show this help message and exit
-j J Deprecated. Use -JOBNAME instead.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-SAVE Return zip archive of job directory at job completion.
-NOJOBID Run the job directly, without Job Control layer.
-JOBNAME JOBNAME Provide an explicit name for the job.