CCS calculation
Structure File
In this example, we calculate the CCS value for the Ubiquitin protein (PDB-ID: 1UBQ) The structure may be downloaded from the Protein Data Bank
wget https://files.rcsb.org/download/1ubq.pdb
MassCCS support molecule file in PQR and XYZ-like format.
Before calculating the CCS by the MassCCS software, it is necessary to assign partial charges to the atoms of the PDB structure file. To address this issue, we can use the PDB2PQR software package that provides a utility for converting protein files from PDB format to PQR format. With no installation PDB2PQR can be used free of charge through the web server PDB2PQR server. For more information about PDB2PQR tool you can visit: https://pdb2pqr.readthedocs.io/en/latest/ .
For the case of ubiquitin, when we select pH=4.0 in the PDB2PQR web server and AMBER forcefield, we generate a PQR file where the total charge of the protein is +4e.
Note
Before the CCS calculation by the MassCCS software, we recommend relax the PDB structures by means energy minimization.
Parameter Input File
It is necessary to use the following input parameter file, in json format, to run MassCCS:
{
"targetFileName": "1ubq.pqr", # Input structure file name in PQR format
"numberProbe" : 10000, # number of trajectories calculations per CCS integral
"nIter" : 10, # number of CCS of Monte Carlo integration
"seed" : 2104, # random seed
"dt" : 10.0, # time step in fs
"Temp" : 298.0, # temperature of buffer gas in Kelvin
"skin" : 0.01, # skin size of unit cell in Angstrom
"GasBuffer" : "He", # buffer gas type
"Equipotential" : "no", # equipotential calculation
"Short-range cutoff" : "yes", # apply cutoff on Lennard-Jones forces
"LJ-cutoff" : 12.0, # radius cutoff in Angstrom
"Long-range forces" : "yes", # apply long-range forces
"Long-range cutoff" : "yes", # apply cutoff on long-range forces
"Coul-cutoff" : 25.0, # radius cutoff in Angstrom
"polarizability" : "yes" # apply polarizability
}
Run Simulation
To run the simulation execute the following command:
cd .. # need to execute massccs from root dir
./build/massccs ./input.json
If your structure is in PQR or XYZ format is only necessary include in the input.json file and run the simulation.
Output
We run this exemple (ubquitin) on CPU consisting of a Dual Intel Xeon E5-2630 v3 processor with 4 cores each and AVX2, running at 2.4 GHz.
The ouput printed on screen is:
*********************************************************
INPUT:: Simulation Parameters
*********************************************************
target filename : 1ubq.pqr
number of probe : 10000
number of iterarions : 10
number of threads : 4
seed number : 2104
gas buffer : He
Target Temperature (K) : 298
timestep (fs) : 10
Skin cell size (Ang) : 0.01
Equipotential : no
Cut short-range interaction : yes
LJ cutoff (Ang) : 12
Apply long-range interaction : yes
Cut long-range interaction : yes
Coulomb cutoff (Ang) : 25
Apply induced-dipole interaction : yes
alpha (Ang^3) : 0.204956
*********************************************************
MOLECULE:: orientation around the inertia principal axis
*********************************************************
Inertia matrix a.u. Ang^2:
{ 812646 -103409 -125747 }
{ -103409 803376 -61197.4 }
{ -125747 -61197.4 758127 }
Rotation matrix applied to molecule:
{ 0.798187 -0.433666 -0.418128 }
{ 0.59767 0.48319 0.639779 }
{ -0.0754147 -0.760566 0.644865 }
Molecule radius: 25.7711 Ang
orientation time of molecule target: 0.0164136 s
target mass: 8568.9 amu
gas mass: 4.0026 amu
reduce mass: 4.00073 amu
charge state: 4 e
*********************************************************
Geometric Ellipsoid:
*********************************************************
maximal distances: 13.3257 15.9013 24.8827 Ang
Initial axis length: 63.3357 65.9113 74.8927 Ang
Ellipsoid axis length: 65.0857 67.6613 76.6427 Ang
ellipsoid calculation time: 7.5278e-05 s
maximal impact parameter: 76.6427 Ang
*********************************************************
Linked-cell
*********************************************************
Numbers of cells: 1716
Nx: 11 Ny: 12 Nz: 13
Filled cells: 29
Empty cells: 1687
Average atoms per cell: 42.5862
Maximum atoms per cell: 194
Minimum atoms per cell: 1
Simulation box:
lx: 132.11 Ang
ly: 144.12 Ang
lz: 156.13 Ang
linked-cell calculation time: 0.0037535 s
*********************************************************
Trajectory calculations
*********************************************************
Ntraj: 10000
Nfree: 1756
Nscatter: 8244
Nlost: 0
omega: 1063.65
Ntraj: 10000
Nfree: 1715
Nscatter: 8285
Nlost: 0
omega: 1078.6
:
:
:
Ntraj: 10000
Nfree: 1738
Nscatter: 8262
Nlost: 0
omega: 1135.46
CCS time: 39.3628 s
*********************************************************
average value of CCS = 1126.88 Ang^2
error value of CCS = 21.6755 Ang^2
Total time: 39.3839 s
Program finished...