External packages

Because ProtoSyn does not exist in an isolated bubble but, instead, in a flourishing and ever-growing sea of novel applications and tools for computational chemistry, the External packages submodules attempts to link structures (and simulations) from ProtoSyn to any file format or input type for common and useful external packages.

Gromacs

Gromacs is "a free and open-source software suite for high-performance molecular dynamics and output analysis". ProtoSyn makes available tools to automatically export Pose structures to the correct input formats for Gromacs (including the definition of .itp files with the forcefield parameters for molecular dynamics), or even employ Gromacs tools to manipulate structures directly.

ProtoSyn.GMX.generate_gmx_itp — Function

generate_gmx_itp(pose::Pose, selection::Opt{AbstractSelection}; atomtypes_itp_filename::String = "atomtypes.itp", molecule_itp_filename::String = "molecule.itp", overwrite::Bool = true, keep_temp_files::Bool = false)

Generate an .itp file for the Fragment given by applying the AbstractSelection selection on the given Pose pose. If no selection is provided, the whole Pose pose will be considered as a single entity for .itp generation. This function assumes the selected Fragment is an unusual organic chemical compound and uses acpype external software to identify atomtypes and write an .itp with AMBER forcefield parameters for usage in GROMACS simulations. By default, acpype prints 2 files: the requested .itp (to a file named molecule_itp_filename) and an .itp file with all atomtypes retrieved (to a file named atomtypes_itp_filename). These atomtypes can sometimes be useful to verify the acpype automatic attribution or to include in the final topology. In any of these files are found in the current working directory, the function raises an error. If overwrite is set to true (is, by default), the existing files are overwritten instead. Any temporary files (starting with "jl") and directories and deleted after completion, unless `keeptemp_filesis set totrue(false, by default). It is reccomended that this function is not used to specific organic polymers, such as proteins. Specific ProtoSyn modules (such asPeptides, in this example) should provide more accurate.itp` generation methods.

Note:

Other modules, such as Peptides, may provide generate_gmx_itp methods for specific molecule types (proteins and peptides, in this example).

Examples

julia> ProtoSyn.GMX.generate_gmx_itp(pose, rn"CBZ")
(...)

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ProtoSyn.GMX.add_bounding_box — Function

add_bounding_box(input_filename::String, output_filename::String, size::T, [shape::String = "cubic"], [verbose::Bool = true]) where {T <: AbstractFloat}

Employ gmx editconf to add a bouding box to a given input file (input_filename), outputs to output_filename. The box has the provided shape and size (in nm). If verbose is set to false (true, by default), hide the GROMACS output.

Examples

julia> ProtoSyn.GMX.add_bounding_box("md.pdb", "md_box.pdb", 1.0)
(...)

source

ProtoSyn.GMX.add_solvent — Function

add_solvent(input_filename::String, output_filename::String, [solvent_type::String = "spc216"], [topol_filename::String = "topol.top"], [verbose::Bool = true])

Employ gmx solvate to add a solvent to a given input file (input_filename), outputs to output_filename. The file contents should be incorporated in a bounding box (see add_bounding_box). The solvent used in given by solvent_type (GROMCAS searchs the current working directory and the default instalation directory for .gro files with this name containing structural information of the solvent molecule). Add solvent information (such as number of added molecules) to the given topol_filename. If verbose is set to false (true, by default), hide the GROMACS output.

Examples

julia> ProtoSyn.GMX.add_solvent("md_box.pdb", "md_sol.pdb")
(...)

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ProtoSyn.GMX.add_ions — Function

add_ions(input_filename::String, output_filename::String; [mdp::String = joinpath(ProtoSyn.resource_dir, "ExternalPackages/GROMACS/mdps/ions.mdp")], [topol_filename::String = "topol.top"], [tpr_filename::String = "ions.tpr"], [positive_ion::String = "NA"], [negative_ion::String = "CL"], [number_of_positive_ions::Int = 0], [number_of_negative_ions::Int = 0], [neutral::Bool = true], [attempt_auto::Opt{Int} = nothing], [verbose::Bool = true])

Employ `gmx genion` to add ions to a given input file

(input_filename), outputs to output_filename. The file contents should be incorporated in a solvated bounding box (see add_bounding_box and add_solvent). Adds number_of_negative_ions of negative_ion and number_of_positive_ions of positive_ion. Optionally, if neutral is set to true, gmx genion will add either positive_ion or negative_ion instances until neutral charge is achieved (reccomended). As a middle step, gmx genion uses the given ions mdp file and writes a temporary tpr_filename. Add ions information (such as number of added molecules) to the given topol_filename. If verbose is set to false (true, by default), hide the GROMACS output. If an attempt_auto is given, automatically chooses the SOL group for ion replacement (interactive, by default). Note that depending on the system, the SOL group number changes. For example, for a protein with ligand, the SOL group should be 15.

Examples

julia> ProtoSyn.GMX.add_ions("md_sol.pdb", "md_ready.pdb", attempt_auto = 15)
(...)

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