def OptimizeRMSD(param):
FF_param['equilibrium']['c3-c3'] = param[0]
FF_param['equilibrium']['c3-f'] = param[1]
FF_param['equilibrium']['cb-c3'] = param[2]
FF_param['equilibrium']['cb-cb'] = param[3]
FF_param['equilibrium']['c3-c3-c3'] = 110.6 + param[4] * 200
FF_param['equilibrium']['c3-cb-c3'] = 100.16 + param[5] * 200
FF_param['equilibrium']['cb-cb-c3'] = 94.18 + param[6] * 200
print(FF_param)
RMSD = Optimize_MD_AMBER_structure(frcmod_filename,struc,state=state,gen_input=False,struc_out=False,**FF_param)
RMSD = RMSD*conv_pos["Angstrom"]
print(RMSD)
return RMSD
def OptimizeRMSD(param):
# FF_param['equilibrium']['c3-c3'] = param[0]
# FF_param['equilibrium']['c3-f'] = param[1]
# FF_param['equilibrium']['cb-c3'] = param[2]
# FF_param['equilibrium']['cb-cb'] = param[3]
# FF_param['equilibrium']['c3-c3-c3'] = 110.6 + param[4] * 200
# FF_param['equilibrium']['c3-cb-c3'] = 100.16 + param[5] * 200
# FF_param['equilibrium']['cb-cb-c3'] = 94.18 + param[6] * 200
# FF_param['equilibrium']['ca-ca'] = abs(param[0])
# FF_param['equilibrium']['ca-c3'] = abs(param[1])
FF_param['equilibrium']['ca-ca-c3'] = 120.63 + param[0] * 200
FF_param['equilibrium']['ca-c3-c3'] = 112.09 + param[1] * 200
print(param)
print(FF_param)
RMSD = Optimize_MD_AMBER_structure("nab_input.frcmod",
struc,
state=state,
gen_input=False,
struc_out=False,
**FF_param)
RMSD = RMSD * conv_pos["Angstrom"]
print(RMSD)
return RMSD
elif state=='Transition':
struc.esp_trans = np.zeros(struc.nat,dtype='f8')
charges = struc.esp_trans
for ii in range(struc.nat):
if struc.at_type[ii] == 'C':
charges[ii] = FG_charges[0]
elif struc.at_type[ii] == 'F':
charges[ii] = -FG_charges[0]
else:
raise Warning("Unknown atom type in structure")
charges[border_C_indx] = 2*FG_charges[1]
charges[border_F_indx] = -FG_charges[1]
RMSD = Optimize_MD_AMBER_structure(frcmod_filename,struc,state=state,gen_input=True,struc_out=False,**FF_param)
print("RMSD init:",RMSD*conv_pos["Angstrom"],"Angstroms")
def OptimizeRMSD(param):
FF_param['equilibrium']['c3-c3'] = param[0]
FF_param['equilibrium']['c3-f'] = param[1]
FF_param['equilibrium']['cb-c3'] = param[2]
FF_param['equilibrium']['cb-cb'] = param[3]
FF_param['equilibrium']['c3-c3-c3'] = 110.6 + param[4] * 200
FF_param['equilibrium']['c3-cb-c3'] = 100.16 + param[5] * 200
FF_param['equilibrium']['cb-cb-c3'] = 94.18 + param[6] * 200
print(FF_param)
RMSD = Optimize_MD_AMBER_structure(frcmod_filename,struc,state=state,gen_input=False,struc_out=False,**FF_param)
RMSD = RMSD*conv_pos["Angstrom"]
print(RMSD)
return RMSD
struc.esp_trans = np.zeros(struc.nat,dtype='f8')
charges = struc.esp_trans
for ii in range(struc.nat):
if struc.at_type[ii] == 'C':
charges[ii] = FG_charges[0]
elif struc.at_type[ii] == 'F':
charges[ii] = -FG_charges[0]
else:
raise Warning("Unknown atom type in structure")
charges[border_C_indx] = 2*FG_charges[1]
charges[border_F_indx] = -FG_charges[1]
NM_info, indx_orig2new = get_AMBER_MD_normal_modes(struc,state=state,gen_input=True,**FF_param)
RMSD = Optimize_MD_AMBER_structure("nab_input.frcmod",struc,state=state,gen_input=True,struc_out=False,**FF_param)
RMSD = RMSD*conv_pos["Angstrom"]
print(RMSD)
print(indx_orig2new)
def compare_NM(param):
print(param)
FF_param['force']['c3-c3'] = abs(param[0])
FF_param['force']['cb-c3'] = abs(param[1])
FF_param['force']['cb-cb'] = abs(param[2])
FF_param['force']['c3-f'] = abs(param[3])
FF_param['force']['cb-fb'] = FF_param['force']['c3-f']
FF_param['force']['c3-c3-c3'] = abs(param[4])
FF_param['force']['cb-c3-c3'] = FF_param['force']['c3-c3-c3']
FF_param['force']['c3-cb-c3'] = FF_param['force']['c3-c3-c3']
FF_param['force']['cb-cb-c3'] = FF_param['force']['c3-c3-c3']