Forcefields¶
The forcefields are a dump for interactions with their parameters, but also
for atom specific information or residue definitions in the form of a
BuildingBlock
. Objects for modifying residues can be set in form of
BlockModifier
or HydrogenConstructor
.
They’re also involved in dealing with the naming mess we’re observing in the molecular mechanics
community and contain definable renaming rules that can be applied on an
EntityHandle
for renaming from e.g. PDB standard to the forcefield
specific standard. The standard forcefields in OpenStructure are loaded from
the files provided by Gromacs and the “standard” naming is therefore the same.
This has implications for controlling the protonation states for histidine.
If you e.g. want to enforce a d-protonated histidine you have to name
it HISD. Further reading can be found in the
Gromacs Manual
Loading the standard forcefields provided by OpenStructure¶
- LoadCHARMMForcefield()¶
Loads the CHARMM27 forcefield read from Gromacs
- Returns:
The loaded
Forcefield
- LoadAMBERForcefield()¶
Loads the AMBER03 forcefield read from Gromacs
- Returns:
The loaded
Forcefield
Reading forcefields¶
- class FFReader(base_dir)¶
The
FFReader
builds up aForcefield
, that gets updated with every call to the read functions. If the read files contain preprocessor statements as they are used in Gromacs, they will be applied to all subsequent lines read in. Parsed preprocessor statements are: #include, #define, #ifdef, #ifndef, #else and #endifNote that this class is rather experimental. It has nevertheless been thoroughly tested for loading the CHARMM and AMBER forcefields in the Gromacs format. The reader is capable of resolving the preprocessor statements as they are used in Gromacs.
- Parameters:
base_dir (
str
) – Base path of the reader. All loaded files must be defined relative to this base path.
- ReadGromacsForcefield()¶
Searches and reads the forcefield.itp and atomtypes.atp files in the base_dir given at initialization. All atom specific informations and bonded as well as nonbonded forces are read this way.
- ReadResidueDatabase(basename)¶
Searches and reads all files belonging the the residue database defined by basename. With basename=aminoacids this function searches and reads all files in the base_dir matching aminoacids.x where x is .rtp .arn .hdb .n.tdb .c.tdb .vsd .r2b. Only the rtp file is mandatory, all others are neglected if not present.
- Parameters:
basename (
str
) – Basename of residue database to be loaded
- ReadITP(basename)¶
Searches and reads the itp file in the base_dir. basename=amazing_ion would therefore load the file amazing_ion.itp
- Parameters:
basename (
str
) – Basename of itp file to be loaded
- SetForcefield(forcefield)¶
Resets reader internal forcefield. Everything read so far is lost, except the already read preprocessor statements.
- Parameters:
forcefield (
Forcefield
) – Forcefield to be set
- GetForcefield()¶
Get the forcefield with everything read so far.
- Returns:
The reader internal
Forcefield
path = "path_to_gromacs/share/top/charmm27.ff" reader = FFReader(path) #read in the data given in forcefield.itp and atomtypes.atp reader.ReadGromacsForcefield() #we also want to read several residue databases reader.ReadResidueDatabase("aminoacids") reader.ReadResidueDatabase("rna") reader.ReadResidueDatabase("dna") #ions and water are also nice to have, they're stored in itp files reader.ReadITP("tip3p") reader.ReadITP("ions") #let's finally get the reader internal forcefield out ff = reader.GetForcefield() #there is also an amazing ion definition in some other directory new_reader = FFReader("path/to/directory/with/itp/files") #we want to modify the previously read forcefield new_reader.SetForcefield(ff) #and read the amazing ion definition from an itp file #note, that any previously defined preprocessor statements #from the previous reader are lost new_reader.ReadITP("amazing_ion") #the new forcefield finally contains everything we need, lets #extract it and save it down ff = new_reader.GetForcefield() ff.Save("charmm_forcefield.dat")
Generating forcefields with Antechamber¶
The antechamber submodule of mol.mm defines functions to use Antechamber (from
AmberTools) to automatically generate force field parameters and load the
results into Forcefield
objects.
Example usage:
from ost.mol import mm
# create parameters for RVP using PDB's component dictionary
mm.antechamber.RunAntechamber('RVP', 'components.cif', base_out_dir='ligands')
# create force field
ff = mm.Forcefield()
ff = mm.antechamber.AddFromPath(ff, 'ligands/RVP')
# equivalent: ff = mm.antechamber.AddFromFiles(ff, 'ligands/RVP/frcmod',
# 'ligands/RVP/out.mpdb')
# since Antechamber cannot deal with ions, you can do it manually
ff = mm.antechamber.AddIon(ff, 'CL', 'CL', 35.45, -1.0, 0.4401, 0.4184)
# save it
ff.Save('ligands/ff.dat')
Functions:
- AddFromFiles(force_field, frcmod_filename, mpdb_filename)¶
Add data from a frcmod and an mpdb file to a force field.
This will add a new
BuildingBlock
to force_field for the residue defined in those files (residue name is extracted from the mpdb file which can only contain a single residue). Charges for each atom are extracted from the mpdb file. According to the frcmod file, anInteraction
is added for each bond, angle, dihedral and improper. Atom types with masses and non-bonded interactions are added to force_field as needed.- Parameters:
force_field (
Forcefield
) – A force field object to which the new parameters are added.frcmod_filename (
str
) – Path tofrcmod
file as generated byparmchk2
.mpdb_filename (
str
) – Path to mpdb file as generated byantechamber
.
- Returns:
The updated force field (same as force_field).
- Return type:
- AddFromPath(force_field, out_dir)¶
Add data from a directory created with
Run()
to a force field. SeeAddFromFiles()
for details.- Parameters:
force_field (
Forcefield
) – A force field object to which the new parameters are added.out_dir (
str
) – Output directory as created withRun()
. Must contain filesfrcmod
andout.mpdb
.
- Returns:
The updated force field (same as force_field).
- Return type:
- AddIon(force_field, res_name, atom_name, atom_mass, atom_charge, lj_sigma, lj_epsilon)¶
Add a single atom as an ion to a force field.
Since Antechamber cannot deal with ions, you can add simple ones easily with this function. This adds a
BuildingBlock
to force_field for the given residue name containing a single atom. The atom will have a type with the same name as the atom name and the given mass, charge and non-bonded (LJ) interaction parameters.- Parameters:
force_field (
Forcefield
) – A force field object to which the ion is added.res_name (
str
) – Residue name for the ion to be added.atom_name (
str
) – Atom name which is also used as atom type name.atom_mass (
float
) – Mass of the atom.atom_charge (
float
) – Charge of the atom.lj_sigma (
float
in nm) – The sigma parameter for the non-bonded LJ interaction.lj_epsilon (
float
in kJ/mol) – The sigma parameter for the non-bonded LJ interaction.
- RunAntechamber(res_name, filename, format='ccif', amberhome=None, base_out_dir=None)¶
Run Antechamber to guess force field parameters for a given residue name.
This requires an installation of AmberTools (tested with AmberTools15) with binaries
antechamber
andparmchk2
.This has the same restrictions as Antechamber itself and we assume the input to be uncharged. Note that Antechamber cannot deal with metal ions and other non-organic elements.
The results are stored in a separate folder named res_name within base_out_dir (if given, otherwise the current working directory). The main output files are
frcmod
andout.mpdb
. The former contains force field parameters and masses. The latter maps atom names to atom types and defines the partial charges. The same output could be obtained as follows:$ antechamber -i <FILENAME> -fi <FORMAT> -bk '<RES_NAME>' -o out.mol2 -fo mol2 -c bcc -pf yes $ parmchk2 -i out.mol2 -f mol2 -o frcmod -a Y $ antechamber -i out.mol2 -fi mol2 -o out.mpdb -fo mpdb -pf yes
The force field parameters can be manually modified if needed. It can for instance happen that some parameters cannot be identified. Those lines will be marked with a comment “ATTN, need revision”.
- Parameters:
res_name (
str
) – Residue name for which we desire force field parameters.filename (
str
) – Path to a file which contains the necessary information for res_name. It must include all hydrogens.format (
str
) – Format of file given with filename. Common formats are ‘ccif’ for PDB’s component dictionary or ‘pdb’ for a PDB file containing the desired residue with all hydrogens.amberhome (
str
) – Base path of your AmberTools installation. If not None, we look forantechamber
andparmchk2
withinAMBERHOME/bin
additionally to the system’sPATH
.base_out_dir (
str
) – Path to a base path, where the output will be stored. If None, the current working directory is used.
The Forcefield Class¶
- class Forcefield¶
- Save(filename)¶
Dumps forcefield into a binary file on disk
- Parameters:
filename (
str
) – Filename of the saved forcefield
- static Load(filename)¶
reads in binary forcefield file
- Parameters:
filename (
str
) – Filename of the forcefield to be loaded- Returns:
loaded
Forcefield
- Raises:
RuntimeError
when filename can’t be found
- AddBond(bond)¶
- Parameters:
bond (
Interaction
) – Bond to be added- Raises:
RuntimeError
when given interaction has no bond specific FuncType
- AddAngle(angle)¶
- Parameters:
angle (
Interaction
) – Angle to be added- Raises:
RuntimeError
when given interaction has no angle specific FuncType
- AddDihedral(dihedral)¶
- Parameters:
dihedral (
Interaction
) – Dihedral to be added- Raises:
RuntimeError
when given interaction has no dihedral specific FuncType
- AddImproper(improper)¶
- Parameters:
improper (
Interaction
) – Improper to be added- Raises:
RuntimeError
when given interaction has no improper specific FuncType
- AddCMap(cmap)¶
- Parameters:
cmap (
Interaction
) – CMap to be added- Raises:
RuntimeError
when given interaction has no cmap specific FuncType
- AddImplicitGenborn(gb)¶
- Parameters:
gb (
Interaction
) – GB to be added- Raises:
RuntimeError
when given interaction has no gb specific FuncType
- AddLJ(lj)¶
- Parameters:
lj (
Interaction
) – LJ to be added- Raises:
RuntimeError
when given interaction has no lj specific FuncType
- AddLJPair(lj_pair)¶
- Parameters:
lj_pair (
Interaction
) – LJPair to be added- Raises:
RuntimeError
when given interaction has no lj_pair specific FuncType
- AddConstraint(constraint)¶
- Parameters:
constraint (
Interaction
) – Constraint to be added- Raises:
RuntimeError
when given interaction has no constraint specific FuncType
- AddMass(type, mass)¶
- Parameters:
type (
str
) – Type of atommass (
float
) – Its mass
- SetFudgeLJ(factor)¶
- Parameters:
factor (
float
) – Factor with which the 1,4 Lennard Jones term should be dampened
- SetFudgeQQ(factor)¶
- Parameters:
factor (
float
) – Factor with which the 1,4 electrostatic term should be dampened
- SetGenPairs(gen_pairs)¶
- Parameters:
gen_pairs (
bool
) – If set to false, all 1,4 interactions must be set with AddLJPair. The Lorentz-Berthelot rule gets used otherwise.
- AddResidueRenamingRule(name, ff_main_name, ff_n_ter_name, ff_c_ter_name, ff_two_ter_name)¶
- Parameters:
name (
str
) – Original name of the residue (e.g. PDB/Gromacs standard)ff_main_name (
str
) – Forcefield specific residue nameff_n_ter_name (
str
) – Forcefield specific name if the residue is N-Terminalff_c_ter_name (
str
) – Forcefield specific name if the residue is C-Terminalff_two_ter_name (
str
) – Forcefield specific name if the residue is N- and C-Terminal
- AddAtomRenamingRule(res_name, old_atom_name, new_atom_name)¶
- Parameters:
res_name (
str
) – Forcefield specific name of the residue the atom belongs toold_atom_name (
str
) – Atom name in PDB/Gromacs standardnew_atom_name (
str
) – FF specific atom name
- AddBuildingBlock(name, block)¶
- Parameters:
name (
str
) – Name of residue thisBuildingBlock
is supposed to be related toblock (
BuildingBlock
) – BuildingBlock to be added
- AddHydrogenConstructor(name, h_constructor)¶
- Parameters:
name (
str
) – Name of residue thisHydrogenConstructor
is supposed to be related toh_constructor (
HydrogenConstructor
) – HydrogenConstructor to be added
- AddBlockModifier(name, modifier)¶
- Parameters:
name (
str
) – Name of residue thisBlockModifier
is supposed to be related tomodifier (
BlockModifier
) – BlockModifier to be added
- SetStandardCTer(res_name, ter_name)¶
Setting a standard CTer influences the behaviour of the GetCTerModifier function. If no specific block modifier is defined there, this is the one that gets returned.
- Parameters:
res_name (
str
) – Forcefield specific residue name this block modifier is supposed to be related toter_name (
str
) – Name of the default c-terminal block modifier for this residue
- SetStandardNTer(res_name, ter_name)¶
Setting a standard NTer incluences the behaviour of the GetNTerModifier function. If no specific block modifier is defined there, this is the one that gets returned.
- Parameters:
res_name (
str
) – Forcefield specific residue name this block modifier is supposed to be related toter_name (
str
) – Name of the default n-terminal block modifier for this residue
- AssignFFSpecificNames(ent[, reverse = False])¶
This function does the forcefield specific renaming magic. It takes the given
EntityHandle
and applies the rules set in AddResidueRenamingRule and AddAtomRenamingRule.- Parameters:
ent (
EntityHandle
) – Entity to be renamedreverse (
bool
) – If False, the function does the renaming from PDB/Gromacs naming to the forcefield specific naming. If True, the opposite happens.
- GetBond(type1, type2)¶
- Parameters:
type1 (
str
) – Type of interacting particle 1type2 (
str
) – Type of interacting particle 2
- Returns:
an
Interaction
with a bond FuncType- Raises:
RuntimeError
when noInteraction
matching given types can be found
- GetAngle(type1, type2, type3)¶
- Parameters:
type1 (
str
) – Type of interacting particle 1type2 (
str
) – Type of interacting particle 2type3 (
str
) – Type of interacting particle 3
- Returns:
an
Interaction
with a angle FuncType- Raises:
RuntimeError
when noInteraction
matching given types can be found
- GetDihedrals(type1, type2, type3, type4)¶
Several dihedral definitions can be merged to one dihedral function. This function therefore returns a list. In a first step all dihedrals matching the given types are gathered and returned. If no dihedrals can be found, the search continues by including wildcard characters in the atom types (X). All found dihedrals matching with all possible combinations of wildcards are then gathered and returned.
- Parameters:
type1 (
str
) – Type of interacting particle 1type2 (
str
) – Type of interacting particle 2type3 (
str
) – Type of interacting particle 3type4 (
str
) – Type of interacting particle 4
- Returns:
a
list
ofInteraction
objects with dihedral FuncType matching given types- Raises:
RuntimeError
when noInteraction
matching given types can be found
- GetImpropers(type1, type2, type3, type4)¶
The same search strategy as in GetDihedrals is used to extract the impropers.
- Parameters:
type1 (
str
) – Type of interacting particle 1type2 (
str
) – Type of interacting particle 2type3 (
str
) – Type of interacting particle 3type4 (
str
) – Type of interacting particle 4
- Returns:
a
list
ofInteraction
objects with improper FuncType matching given types- Raises:
RuntimeError
when noInteraction
matching given types can be found
- GetCMap(type1, type2, type3, type4, type5)¶
- Parameters:
type1 (
str
) – Type of interacting particle 1type2 (
str
) – Type of interacting particle 2type3 (
str
) – Type of interacting particle 3type4 (
str
) – Type of interacting particle 4type5 (
str
) – Type of interacting particle 5
- Returns:
an
Interaction
with a cmap FuncType- Raises:
RuntimeError
when noInteraction
matching given types can be found
- GetImplicitGenborn(type)¶
- Parameters:
type (
str
) – Type of particle- Returns:
an
Interaction
with a gb FuncType- Raises:
RuntimeError
when noInteraction
matching given type can be found
- GetLJ(type)¶
- Parameters:
type (
str
) – Type of particle- Returns:
an
Interaction
with a lj FuncType- Raises:
RuntimeError
when noInteraction
matching given type can be found
- GetLJ(type1, type2[, pair=False])¶
- Parameters:
type1 (
str
) – Type of interacting particle 1type2 (
str
) – Type of interacting particle 2pair (
bool
) – If set to true, the interaction is assumed to be a 1,4-interaction and the set lj_pairs are first searched for matches. In case of no success, the function uses the Lorentz-Berthelot rule to combine the sigma and epsilon parameters. If set to false, the Lorentz-Berthelot rule is applied directly.
- Raises:
RuntimeError
when noInteraction
matching given types can be found or when pair is true and no appropriate lj_pair is set despite gen_pair flag being false.
- GetConstraint(type1, type2)¶
- Parameters:
type1 (
str
) – Type of interacting particle 1type2 (
str
) – Type of interacting particle 2
- Returns:
an
Interaction
with a constraint FuncType- Raises:
RuntimeError
when noInteraction
matching given types can be found
- GetMass(type)¶
- Parameters:
type (
str
) – Type of particle- Returns:
float
- the mass- Raises:
RuntimeError
if no mass has been set for this atom type
- GetFudgeLJ()¶
- Returns:
float
- Factor with which the 1,4 Lennard Jones term should be dampened
- GetFudgeQQ()¶
- Returns:
float
- Factor with which the 1,4 electrostatic term should be dampened
- GetAtomType(res_name, atom_name)¶
- Parameters:
res_name (
str
) – Forcefield specific residue nameatom_name (
str
) – Forcefield specific atom name belonging to that residue
- Returns:
str
- atom type- Raises:
RuntimeError
if forcefield has no suchBuildingBlock
or when atom is not present in thatBuildingBlock
- GetHydrogenConstructor(res_name)¶
- Parameters:
res_name (
str
) – Name of residue- Returns:
HydrogenConstructor
for this name, invalid if it can’t be found
- GetBuildingBlock(res_name)¶
- Parameters:
res_name (
str
) – Name of residue- Returns:
BuildingBlock
for this name, invalid if it can’t be found
- GetBuildingBlockNames()¶
- Returns:
list
of all building block names present in that forcefield
- GetBlockModifier(res_name)¶
- Parameters:
res_name (
str
) – Name of residue- Returns:
BlockModifier
for this name, invalid if it can’t be found
- GetNTerModifier(res_name[, ter_name=""])¶
- Parameters:
res_name (
str
) – Name of residueter_name (
str
) – If not set, the ter_name defined by SetStandardNTer gets used
- Returns:
BlockModifier
for this name, invalid if it can’t be found
- GetCTerModifier(name[, ter_name=""])¶
- Parameters:
res_name (
str
) – Name of residueter_name (
str
) – If not set, the ter_name defined by SetStandardCTer gets used
- Returns:
BlockModifier
for this name, invalid if it can’t be found