Dear Jason,
I’m trying out a simple organic molecule for the explicit solvent CpHMD simulation.
H-O=C-O
|
CH3-C-CH3
|
CH3
I used partial charges from OPLS and calculated the reference energy for the deprotonated form with sander TI method (IGB 2). I added this molecule to the residue list in Cpinutil.py and Residues.py (in cpinutils dir) as per AMBER 15 manual.
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Cpinutil.py :
LINE 257: change(parm, 'RADII', ':PTN.O=,.OZ=', 1.3).execute()
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Residue.py:
# PTN
refene1 = _ReferenceEnergy(igb2=0)
refene1.solvent_energies()
refene1.dielc2_energies(igb2=0)
refene1.dielc2.solvent_energies()
refene2 = _ReferenceEnergy(igb2=-44.8284)
refene2.solvent_energies()
refene2.dielc2_energies()
refene2.dielc2.solvent_energies()
refene2.set_pKa(5.03, deprotonated=True)
PTN = TitratableResidue('PTN', ['CB', 'HB2', 'HB3', 'HB4', 'CA', 'CB5', 'HB6', 'HB7', 'HB8', 'CB9', 'HB10', 'HB11', 'HB12', 'C', 'O', 'OZ', 'H'], pka=5.03)
PTN.add_state(protcnt=1, refene=refene1, # protonated
charges=[-0.180, 0.600, 0.600, 0.600, 0.000, -0.180, 0.600, 0.600, 0.600, -0.180, 0.600, 0.600, 0.600, 0.520, -0.440, -0.530, 0.450])
PTN.add_state(protcnt=0, refene=refene2, # deprotonated
charges=[-0.180, 0.600, 0.600, 0.600, -0.100, -0.180, 0.600, 0.600, 0.600, -0.180, 0.600, 0.600, 0.600, 0.700, -0.800, -0.800, 0.000])
PTN.check()
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I also added this residue under amino acid list in residues.py file & titratable_residues.py (AmberTools/src/parmed/chemistry/amber).
I tried to generate the cpin file for the organic molecule but I run into "residue not titratable" cpin error. I’m not sure what other supplementary files I need to modify to make it work. I would really appreciate your help.
Thanks,
Arsh
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Received on Tue Aug 25 2015 - 17:00:03 PDT
