External packages

The External packages is a submodule of ProtoSyn.Peptides module. As such, the following section introduces both new types and methods that work together, in a generally independent way from the rest of the module, and require an unique exploratory section on their own.

As futher explained in the Core module External packages section, ProtoSyn makes available tools to define and manipulate input structures for common and useful external packages.

Gromacs

For the Gromacs simulation suite, the Peptides module introduces methods to define .itp files for protein structures, as well as manipulate the Pose graph to match both the Atom names and Atom order expected by Gromacs.

ProtoSyn.Peptides.GMX.generate_gmx_itp — Function

generate_gmx_itp(pose::Pose, [selection::Opt{AbstractSelection} = nothing]; [molecule_itp_filename::String = "protein.itp"], [overwrite::Bool = true], [keep_temp_files::Bool = false], [gmx_histidine_type::Int = 0], [gmx_water_model::String = "tip3p"], [gmx_forcefield::String = "amber99sb-ildn"])

Generate a protein .itp file for usage in Gromacs using the gmx pdb2gmx utility program with forcefield parameters for the given Pose pose. If an AbstractSelection selection is provided, only the selected Atom instances will be considered (in a Fragment) for .itp generation. Note that since gmx pdb2gmx is being used, non-protein Residue instance may cause problems or undesired parameters in the resulting .itp file. It is reccomended to select protein Residue instances only. The .itp data will be written to molecule_itp_filename (if file exists, setting overwrite to true will overwrite any existing file with the same name, set to true by default). Setting keep_temp_files to true (false, by default) prevents ProtoSyn from deleting any temporary files and directories generated during the method call (this includes Gromacs backups ending with "#" and any file or directory starting with "jl_"). During gmx pdb2gmx call, automatically sets:

Histidines to be of type gmx_histidine_type (default: 0);
Water model to be of type gmx_water_model (default: "tip3p");
Forcefield to be of type gmx_forcefield (default: "amber99sb-ildn").

See also

generate_gmx_topology

Examples

julia> ProtoSyn.Peptides.GMX.generate_gmx_itp(pose)
✓ All necessary packages were found!
 (...)

source

ProtoSyn.Peptides.GMX.generate_gmx_topology — Function

generate_gmx_topology(pose::Pose; [protein_itp_filename::String = "protein.itp"], [atomtypes_itp_filename::String = "atomtypes.itp"], [molecule_itp_filename::String = "molecule.itp"], [overwrite::Bool = true], [keep_temp_files::Bool = false], [gmx_histidine_type::Int = 0], [gmx_water_model::String = "tip3p"], [gmx_forcefield::String = "amber99sb-ildn"], [topology_filename::String = "topol.top"], [include_atomtypes::Bool = false])

Generate a system .top file for usage in Gromacs (using the gmx pdb2gmx and acpype utility programs) with forcefield parameters for the given Pose pose. This method automatically tries to select protein Residue instances using the ProteinSelection. The selected Residue instances forcefield parameters will be compiled into protein_itp_filename using the gmx pdb2gmx utility program (if file exists, setting overwrite to true will overwrite any existing file with the same name, set to true by default). During gmx pdb2gmx call, automatically sets:

Histidines to be of type gmx_histidine_type (default: 0);
Water model to be of type gmx_water_model (default: "tip3p");
Forcefield to be of type gmx_forcefield (default: "amber99sb-ildn").

Any remaining Residue instances will be considered as ligand molecules, and the forcefield information will be compiled into molecule_itp_filename and atomtypes_itp_filename using the acpype utility program. Setting keep_temp_files to true (false, by default) prevents ProtoSyn from deleting any temporary files and directories generated during the method call (this includes Gromacs backups ending with "#" and any file or directory starting with "jl"). The resulting .itp files are combined into the final `topologyfilename.top file (ifinclude_atomtypesis set totrue, the ligand molecule's atomtypes file is also included in the topology,false` by default).

Note:

This method is untested on proteins with multiple ligands and may fail. This may change in future versions of ProtoSyn.

See also

generate_gmx_itp generate_gmx_files

Examples

julia> ProtoSyn.Peptides.GMX.generate_gmx_topology(pose)
✓ All necessary packages were found!
 (...)

source

ProtoSyn.Peptides.GMX.sort_atoms_and_graph_gmx! — Function

sort_atoms_and_graph_gmx!(pose::Pose)

Sorts Atom instances in the encompassing AbstractContainer structures and the resulting Graph for Gromacs simulations (Gromacs expects a given atom order to match with the gmx pdb2gmx and acpype generated .itp and .top files - this does not necessarilly match the IUPAC conventions).

Examples

julia> ProtoSyn.Peptides.GMX.sort_atoms_and_graph_gmx!(pose)
Pose{Topology}(Topology{/2a3d:60945}, State{Float64}:
 Size: 1140
 i2c: false | c2i: false
 Energy: Dict(:Total => Inf)
)

source

ProtoSyn.Peptides.GMX.GMXS — Constant

(ProtoSyn.Peptides.GMX.GMXS)(atom::Atom, stack::Vector{Atom})

Gromacs-like algorithm for travel_graph. Correctly sorts the given Atom atom children instances and concatenates with the current stack as expected by the Gromacs external package.

Examples

julia> ProtoSyn.Peptides.GMX.GMXS(pose.graph[1, 1, 1], Vector{Atom}())
4-element Vector{Atom}:
 Atom{/2a3d:34300/A:1/MET:1/H1:2}
 Atom{/2a3d:34300/A:1/MET:1/H2:3}
 Atom{/2a3d:34300/A:1/MET:1/H3:4}
 Atom{/2a3d:34300/A:1/MET:1/CA:5}

source

ProtoSyn.Peptides.GMX.assign_gmx_atom_names! — Function

assign_gmx_atom_names!(pose::Pose, selection::Opt{AbstractSelection} = nothing)

Rename Atom instances in the given Pose pose to match with the gmx pdb2gmx and acpype generated .itp and .top files - this does not necessarilly match the IUPAC conventions. If an AbstractSelection selection is provided, consider only the selected Atom instances (any given selection will be promoted to be of Atom type - see ProtoSyn.promote).

Examples

julia> ProtoSyn.Peptides.GMX.assign_gmx_atom_names!(pose)
Pose{Topology}(Topology{/2a3d:55318}, State{Float64}:
 Size: 1140
 i2c: false | c2i: false
 Energy: Dict(:Total => Inf)
)

source

ProtoSyn.Peptides.GMX.generate_gmx_files — Function

generate_gmx_files(pose::Pose; protein_itp_filename::String ="protein.itp", output_pdb_filename::String ="system.pdb", atomtypes_itp_filename::String ="atomtypes.itp", molecule_itp_filename::String ="molecule.itp", overwrite::Bool =true, keep_temp_files::Bool =false, gmx_histidine_type::Int =0, gmx_water_model::String ="tip3p", gmx_forcefield::String ="amber99sb-ildn", topology_filename::String ="topol.top", include_atomtypes::Bool =false)

Generate all the necessary files to launch a Gromacs MD simulation (.top, .itp and correctly ordered/named .pdb files). For topology generation, please check generate_gmx_topology documentation: all arguments used in that method are also input arguments of this one. For .pdb generation, ProtoSyn attempts to sort (using sort_atoms_and_graph_gmx!) and rename (using assign_gmx_atom_names!) Atom instances in accordance to the expected values in Gromacs before exporting the given Pose pose to a output_pdb_filename file. Check these methods documentation for more details.

Examples

julia> ProtoSyn.Peptides.GMX.generate_gmx_files(pose)
✓ All necessary packages were found!
 (...)

source