IL_simulations

Scripts to create directories with the required files for molecular dynamics simulations of systems with proteins and ionic liquid solutions. Here, the topol.top files are created for the protein Ubiquitin and using the ff OPLS-VSIL avaiable at...

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1 - directories of PDB and FF files

# example of input

using IL_simulations, PDBTools

top_dir     =  "/home/viniciusp/Documents/doutorado/ANALYSE/Repository/IL_simulations.jl/VSIL/ITP"
pdb_dir     =  "/home/viniciusp/Documents/doutorado/ANALYSE/Repository/IL_simulations.jl/VSIL/PDB"
input_dir   =  "/home/viniciusp/Documents/doutorado/ANALYSE/Repository/IL_simulations.jl/ubiquitin_files"
top_ion_dir =  "/home/viniciusp/Documents/doutorado/ANALYSE/Repository/IL_simulations.jl/ion_files"


atoms   = readPDB("$input_dir/ubq.pdb")
MMP     = mass(atoms)

#cation1 = "BMIM"
#anion1  = "NO3"
#anion2  = "DCA"

function molarmass(anion, cation, pdb_dir)
  atcation = readPDB("$pdb_dir/$(cation)_VSIL.pdb")
  atanion  = readPDB("$pdb_dir/$(anion)_VSIL.pdb")
  MMIL = mass(atcation) + mass(atanion)
  return MMIL
end

#MMIL  = molarmass(anion1, cation1, pdb_dir)
#MMIL2 = molarmass(anion2, cation1, pdb_dir)
#c       =  0.10
#
### test with one IL/salt and a protein/polymer
##cd("PONEIL")
##newil = EMIMCL
#
cation = "EMIM"
anion  = "Cl"
il     = "$(cation)$(anion)"
MMIL = IL_simulations.molarmass(anion, cation, pdb_dir)
dir = pwd();
for i in ["0.50", "1.00", "1.50", "2.00", "2.50", "3.00"]
  for j in ["00", "01", "02", "03", "04", "05", "06", "07", "08", "09", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19","20"]
    cd("$dir/$il/$i/$j")
    conc = parse(Float64,i)
    data = IL_simulations.Data_il(protein="$input_dir/ubq.pdb", MMP = MMP, cation = cation, anion = anion,MM = MMIL,c=conc)
    nions, nwater, sides = prot_elec(data)
    IL_simulations.top(dict, top_dir, input_dir, data, nions, nwater)
    IL_simulations.pack_input(data,pdb_dir,nions,nwater,sides)
    IL_simulations.mdp_files_solute()
    IL_simulations.posre(input_dir)
    IL_simulations.analyzeIN(pdb_dir,data)
  end
end






## mixed system
#cation = "EMIM"
#anion1  = "Cl"
#anion2 = "NO3"
#il = "$(cation)$(anion1)$(anion2)"
#MMIL1 = molarmass(anion1, cation, pdb_dir)
#MMIL2 = molarmass(anion2, cation, pdb_dir)
#dir = pwd();
#for i in ["0.50", "1.00", "1.50", "2.00", "2.50", "3.00"]
#  for j in ["00", "01", "02", "03", "04", "05", "06", "07", "08", "09", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19","20"]
#    cd("$dir/$il/$i/$j")
#    conc = parse(Float64,i)
#    data = IL_simulations.Data_2il(protein="$input_dir/ubq.pdb", MMP = MMP, cation = cation, anion1 = anion1, anion2 = anion2, MM1 = MMIL1, MM2 = MMIL2 , c=conc)
#    ncat, nan, nwater, sides = prot_melec(data)
#    println("data for the simulation")
#    println("ncations = $ncat")
#    println("nanions = $nan and $nan")
#    IL_simulations.top(dict, top_dir, input_dir, data, ncat, nan, nwater)
#    println("passou da topologia")
#    IL_simulations.pack_input(data,pdb_dir, ncat, nan, nwater,sides)
#    IL_simulations.mdp_files_solute(input_dir)
#    IL_simulations.posre(input_dir)
#    IL_simulations.analyzeIN2(pdb_dir,data)
#  end
#end