Dear all,
I am trying to recreate the values of reference energies that are described
in titratable_residues.py and I would appreciate some clarification on this
matter.
Taking TYR as example:
# Tyrosine
refene2 = _ReferenceEnergy(igb2=-65.113428, igb5=-64.166385,
igb8=-61.3305355)
refene2.solvent_energies(igb2=-65.003415, igb5=-64.047229)
refene2.dielc2_energies(igb2=-32.167520, igb5=-31.751177)
refene2.dielc2.solvent_energies()
refene2.set_pKa(9.6, deprotonated=True)
TYR = TitratableResidue('TYR', ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3',
'CG',
'CD1', 'HD1', 'CE1', 'HE1', 'CZ', 'OH', 'HH', 'CE2',
'HE2', 'CD2', 'HD2', 'C', 'O'], pka=9.6)
TYR.add_state(protcnt=1, refene=refene1, # protonated
charges=[-0.4157, 0.2719, -0.0014, 0.0876, -0.0152, 0.0295,
0.0295, -0.0011, -0.1906, 0.1699, -0.2341, 0.1656, 0.3226,
-0.5579, 0.3992, -0.2341, 0.1656, -0.1906, 0.1699, 0.5973,
-0.5679])
TYR.add_state(protcnt=0, refene=refene2, # deprotonated
charges=[-0.4157, 0.2719, -0.0014, 0.0876, -0.0858, 0.0190,
0.0190, -0.2130, -0.1030, 0.1320, -0.4980, 0.1320, 0.7770,
-0.8140, 0.0, -0.4980, 0.1320, -0.1030, 0.1320, 0.5973,
-0.5679])
TYR.check()
In this case, and preparing the prmtop files for the TI calculation, I used
the charges described above for the protonated and deprotonated forms.
For the TI, one of the inputs used was:
nstlim =5000000, nscm=2000,
ntx=5, irest=1, ntpr=1000,
temp0=300.0, ntt=3, gamma_ln=5.0,
igb=5, saltcon=0.1, nrespa=1, cut=30.0
ntc=2, ntf=2,
dt=0.001,
ntwr = 10000, ntwx=1000, ntave=1000
icfe=1,clambda=0.04794,
With a average result of DV/DL -0.1798.
Using Ref Energy = TI - R*T*ln(10)*pKa I get a value of -5.9172
I would like to ask for thoughts on why this value is so off when compared
whit REF_ENERGY?
Thank you in advance!
Best Regards,
Nuno
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 28 2018 - 07:00:02 PDT
