On Wed, 2014-09-17 at 14:11 -0400, M Olivia Kim wrote:
> Hi Jason,
>
> Thank you very much for the detailed answer. Since I am trying to use an
> implicit solvent model, I computed the _ReferenceEnergy term using TI,
> followed by typing in all the atom names and atomic charges into the
> residues.py script accordingly:
>
>
> # STP
> refene1 = _ReferenceEnergy(igb2=0, igb5=0, igb8=0)
> refene1.solvent_energies()
> refene1.dielc2_energies()
> refene1.dielc2.solvent_energies()
> refene2 = _ReferenceEnergy(igb2=0, igb5=0, igb8=-83.6047)
> refene2.solvent_energies()
> refene2.dielc2_energies()
> refene2.dielc2.solvent_energies()
> refene2.set_pKa(5.2, deprotonated=True)
>
> STP = TitratableResidue('STP', ['C2', 'H2', 'C1', 'H1', 'C5', 'H4', 'N1',
> 'H32', 'C4', 'H3', 'C3', 'C6', 'N3', 'C7', 'H5', 'C8',
> 'H6', 'N2', 'C9', 'N4', 'H7', 'C10', 'C15', 'H10',
> 'C11',
> 'C29', 'H29', 'H30', 'H31', 'C12', 'H8', 'C13', 'H9',
> 'C14', 'N5', 'H11', 'C16', 'O1', 'C17', 'C22', 'C21',
> 'H14', 'H15', 'C18', 'H12', 'C19', 'H13', 'C20',
> 'C23',
> 'H16', 'H17', 'N6', 'C24', 'H18', 'H19', 'C25', 'H20',
> 'H21', 'N7', 'C26', 'H22', 'H23', 'H24', 'C27', 'H25',
> 'H26', 'C28', 'H27', 'H28'], pka=5.2)
> STP.add_state(protcnt=1, refene=refene1, # protonated
> charges=[0.0280, 0.1765, -0.1875, 0.1944, 0.0576, 0.1992,
> -0.2441,
> 0.3707, 0.1533, 0.1729, -0.0609, 0.6793, -0.9497, -0.8008,
> 0.2475,
> 0.5590, 0.0908, -0.7663, 1.1941, -0.7322, 0.4048, 0.1658,
> -0.2871,
> 0.1961, 0.1087, -0.2446, 0.0813, 0.0813, 0.0813, -0.2257,
> 0.1857,
> -0.3276, 0.2012, 0.3540, -0.6426, 0.3197, 0.8032, -0.5972,
> -0.1946,
> -0.1165, -0.1793, 0.1363, 0.1459, -0.1165, 0.1459, -0.1793,
> 0.1363,
> 0.1836, -0.2068, 0.1136, 0.1136, -0.1493, -0.2497, 0.1392,
> 0.1392,
> -0.0799, 0.0993, 0.0993, -0.2388, -0.2242, 0.0984, 0.0984,
> 0.0984,
> -0.0799, 0.0993, 0.0993, -0.2497, 0.1392, 0.1392])
> STP.add_state(protcnt=0, refene=refene2, # deprotonated
> charges=[0.1622, 0.1160, -0.5119, 0.1919, 0.4665, 0.0459,
> -0.6915,
> 0.0000, 0.5046, 0.0454, -0.3953, 0.7772, -0.9263, -0.7760,
> 0.2223,
> 0.4890, 0.0827, -0.7788, 1.1570, -0.7288, 0.3966, 0.1834,
> -0.2969,
> 0.2001, 0.1065, -0.2755, 0.0880, 0.0880, 0.0880, -0.2161,
> 0.1740,
> -0.3502, 0.1925, 0.3551, -0.6481, 0.3136, 0.7933, -0.5879,
> -0.1766,
> -0.1168, -0.1824, 0.1327, 0.1471, -0.1168, 0.1471, -0.1824,
> 0.1327,
> 0.1640, -0.1339, 0.0881, 0.0881, -0.1668, -0.2420, 0.1386,
> 0.1386,
> -0.1029, 0.1057, 0.1057, -0.2352, -0.2196, 0.0956, 0.0956,
> 0.0956,
> -0.1029, 0.1057, 0.1057, -0.2420, 0.1386, 0.1386])
> STP.check()
>
> However, when I use cpinutil.py, the program says "CPIN generation
> complete!", without any warning, while the generated cpin file doesn't have
> any data, like this:
>
> &CNSTPH
> CHRGDAT=
> PROTCNT=
> RESNAME='System: Unknown',
> RESSTATE=
>
> STATENE=
> TRESCNT=0,
> /
>
> I wonder what is wrong with my residues.py. Would you have any idea? Thank
> you.
Don't forget to add the new residue name to the titratable_residues list
at the top of residues.py. That's the list that cpinutil reads from to
determine which residues are titratable.
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 12:00:03 PDT
