from torsionfit import sqlite_plus
from pymc import MCMC
from parmed.charmm import CharmmParameterSet
import glob
from pymc import MCMC
structure = 'pyrrol.psf'
scan = glob.glob('torsion-scan/*.log')
pyrrol_scan = ScanSet.parse_gauss(scan, structure)
pyrrol_opt = pyrrol_scan.extract_geom_opt()
# set up torsionfit model
param_to_optimize = [
('CG331', 'CG321', 'CG321', 'NG3C51'),
('CG321', 'CG321', 'NG3C51', 'CG2R51'),
('CG321', 'CG321', 'NG3C51', 'CG251O'),
('CG2D2', 'CG251O', 'NG3C51', 'CG321'),
]
param = CharmmParameterSet('../charmm_ff/top_all36_cgenff.rtf',
'../charmm_ff/par_all36_cgenff.prm', 'pyrrol.str')
model = Model.TorsionFitModelEliminatePhase(param,
pyrrol_opt,
decouple_n=True,
sample_n5=True,
param_to_opt=param_to_optimize)
db = sqlite_plus.load('pyrrol_4.db')
sampler = MCMC(model.pymc_parameters, db=db)
sampler.restore_sampler_state()
sampler.sample(100000)
