The dockprep command performs several tasks to prepare structures for molecular docking or other calculations, such as:
Many of these steps can be performed separately, but dockprep unites them for convenience. The corresponding tool (graphical interface) is Dock Prep.
memorize none | save | use
Whether to save the current settings of all (other) dockprep options in preferences for future use, or use previously saved options, or neither (none, default).
delSolvent true | false
delIons true | false
Whether to delete water and ions, respectively (both default true). See also: delete
delAltLocs true | false
Whether to delete all but the currently used alternate locations (default true). See also: altlocs clean
Whether and how to repair truncated amino acid sidechains, where method can be any of the following:
- Dunbrack or true (default) – Dunbrack 2010 smooth backbone-dependent rotamer library (5% stepdown; for chain-terminal residues, the Dunbrack 2002 backbone-independent version is used instead)
- Dynameomics – Dynameomics rotamer library
- Richardson.common – common-atom values (author-recommended) from the Richardson backbone-independent rotamer library
- Richardson.mode – mode values from the Richardson backbone-independent rotamer library
- ala – convert amino acid residues with truncated sidechains to alanine (leave only sidechain -CH3)
- gly – convert amino acid residues with truncated sidechains to glycine (remove sidechain entirely)
See also: swapaa, troubleshooting charge addition
Whether to convert certain nonstandard residues to their corresponding standard residues, where list is a list separated by commas only (default 5BU,CSL,UMS,MSE) of one or more of the following residue names:
- 5BU (bromo-UMP) to U (UMP) – change 5-bromouridine-5'-monophosphate to RNA residue uridine-5'-monophosphate by deleting the bromine atom
- CSL (methylselenyl-dCMP) to C (CMP) – change 2'-methylselenyl-2'-deoxycytidine-5'-phosphate to RNA residue cytidine-5'-monophosphate by replacing the methylselenyl moiety with an oxygen atom named O2' and adjusting the bond length to 1.430 Å
- UMS (methylselenyl-dUMP) to U (UMP) – change 2'-methylselenyl-2'-deoxyuridine-5'-phosphate to RNA residue uridine-5'-monophosphate by replacing the methylselenyl moiety with an oxygen atom named O2' and adjusting the bond length to 1.430 Å
- MSE (selenomethionine) to MET (methionine) – change MSE to MET by changing the selenium atom to a sulfur atom named SD and adjusting the CG-SD and SD-CE bond lengths to 1.81 and 1.78 Å, respectively. If not converted, MSE will still get the same partial charges as MET, but the bond lengths will not be changed.
ah true | false [ addh-options ]
Whether to add hydrogens (default true), with further associated options. See also: addh
ac true | false
Whether to add charges (default true). Adding charges requires explicit hydrogens on the structure, either present already or added with the ah option.
acMethod am1-bcc | gasteiger
If adding charges (ac true), which charge calculation method to use for nonstandard residues:
While both methods are much faster than ab initio calculations, the Gasteiger method is the faster and more approximate of the two. See the method option of addcharge for further details.
- am1-bcc (default) – semi-empirical (AM1) with bond charge correction (BCC), parametrized to reproduce ab initio (HF/6-31G*) electrostatic potentials
- gasteiger – iterative partial equalization of orbital electronegativity, a faster method based on atom types and connectivity
Several options only apply to adding hydrogens (ah true) and are identical to the corresponding addh command options except that the keywords start with “ah”:
ahHbond true | false
Whether H-bond formation should also be considered (default true). Considering H-bonds increases calculation time and may not produce a globally optimal network of H-bonds.
ahInIsolation true | false
Whether to use only the atoms within the same model (default true). Otherwise, other models in the vicinity (except sibling submodels of the same model) may affect hydrogen placement, even if the other models were not designated for hydrogen addition. Sibling submodels of the same model (e.g., #1.1, #1.2, #1.3, ...) are always treated in isolation from one another, even if this option is false.
The distance between a heavy atom X and metal ion M (default 3.95 Å) within which to suppress adding a hydrogen to X if both of the following also apply:
- X is electronegative (O or N, but more generally, periodic table groups 15-16)
- the X-H-M angle would be >120°
ahTemplate true | false
Whether to use idealized coordinates to discern atom types in nonstandard residues, instead of their actual coordinates in the structure (default false). The idealized coordinates are looked up by residue name in the PDB Chemical Component Dictionary. Setting template true is useful for structures with poorly (structurally) determined ligands that could be mis-typed, potentially causing addition of the wrong number of hydrogens or hydrogens in incorrect positions.
ahUseAspName true | false
ahUseCysName true | false
ahUseGluName true | false
ahUseHisName true | false
ahUseLysName true | false
By default, if amino acids have standard residue names, each histidine sidechain will be protonated based on its local environment, whereas the sidechains of other residue types will be assigned protonation states reasonable at physiological pH, regardless of the local environment: negative aspartic acid and glutamic acid, positive arginine and lysine, and neutral cysteine and tyrosine. The following command options allow alternative protonation states of certain amino acids to be specified with special residue names:
option true (default) false ahUseHisName HIS unspecified (guess from local environment),
HID δ-nitrogen protonated, HIE ε-nitrogen protonated,
HIP both sidechain nitrogens protonated
all treated as unspecified ahUseAspName ASP negatively charged, ASH neutral (OD2-protonated) all negatively charged ahUseGluName GLU negatively charged, GLH neutral (OE2-protonated) all negatively charged ahUseLysName LYS positively charged, LYN neutral all positively charged ahUseCysName CYS unspecified (guess from local environment),
CYM negatively charged
all treated as unspecified
These names can be assigned to residues beforehand by text-editing the PDB file of the structure before it is opened, or by using the command setattr to change the name residue attribute. The atom types within these amino acids are ignored for hydrogen addition, so changing them to try to control hydrogen addition will have no effect.