modion¶
Usage¶
cg_spica modion INPUT_PDB OUTPUT_PDB [-conc <float>] [-soluq <int>] [-pspica]
Description¶
modion adjusts CG NaCl concentration in simulation systems for SPICA or pSPICA.
This program recognizes atom names W and W1 as SPICA and pSPICA CG water models, respectively.
For ions, the atom names SOD and CLA are recognized as SPICA CG ions,
while the atom names SOD1 and CLA1 are recognized as pSPICA CG ions.
The atom names are given in a CG configuration file in the PDB format.
The -conc option takes a value of the adjusted NaCl concentration after conversion.
The -soluq option takes a total charge of solute molecules contained in the simulation system.
Note that, in SPICA and pSPICA topology files, the point charges, q = +-1, are set to q = +-0.1118 and q = +-0.5590,
respectively, to account for the dielectric constant applied in the models.
For an argument of -soluq, specify a total charge of solute molecules with the point charges of q = +-1.
The argument corresponds to the number of counterions needed for neutralization.
The -pspica option is needed when this program is applied for pSPICA.
Example¶
cg_spica modion prot_memb.cg.pdb prot_memb.cg.200mM.pdb -soluq 4 -conc 0.2
cg_spica modion prot_memb.cg.200mM.pdb prot_memb.cg.500mM.pdb -soluq 4 -conc 0.5
Positional args¶
INPUT_PDB[<.pdb>]Input configuration file in PDB format
OUTPUT_PDB[<.pdb>]Output configuration file in PDB format
Optional args¶
-conc<float> (0.15) [M]Specify NaCl concentration to be reached
-soluq<int> (0) [e]A total charge of solute molecules (the number of counterions for neutralization)
-pspica(off)Apply this program for pSPICA water and ion models (default: for SPICA water and ion models)