[MMTK] Bcdex molecule
=?iso-8859-1?q?Julio=20Rangel=20Mata?=
iori1977@yahoo.com
Thu, 16 Dec 1999 18:11:29 -0600 (CST)
Hi.. i´m Julio and this is my problem
Python 1.5.2 (#1, Oct 20 1999, 17:06:11) [C] on aix4
Copyright 1991-1995 Stichting Mathematisch Centrum, Amsterdam
>>> import solvatacion
139 water molecules will be added
Solvent molecules have been added, now shrinking universe...
Traceback (innermost last):
File "<stdin>", line 1, in ?
File "solvatacion.py", line 60, in ?
MMTK.Solvation.shrinkUniverse(universe, temperature, 'solvation.nc')
File "/usr/local/lib/python1.5/site-packages/MMTK/Solvation.py", line
119, in shrinkUniverse
minimizer(steps = 10)
File "/usr/local/lib/python1.5/site-packages/MMTK/Minimization.py", line
82, in __call__
evaluator = self.universe.energyEvaluator().evaluator.CEvaluator()
File "/usr/local/lib/python1.5/site-packages/MMTK/Universe.py", line
412, in energyEvaluator
subset1, subset2)
File
"/usr/local/lib/python1.5/site-packages/MMTK/ForceFields/ForceField.py",
line 212, in __init__
self.global_data)
File
"/usr/local/lib/python1.5/site-packages/MMTK/ForceFields/MMForceField.py",
line 333, in evaluator
global_data)
File
"/usr/local/lib/python1.5/site-packages/MMTK/ForceFields/ForceField.py",
line 102, in evaluator
global_data))
File
"/usr/local/lib/python1.5/site-packages/MMTK/ForceFields/MMForceField.py",
line 83, in evaluator
global_data)
File
"/usr/local/lib/python1.5/site-packages/MMTK/ForceFields/BondedInteractions.py",
line 45, in evaluator
self.addBondTerm(data, bond, bu, global_data)
File
"/usr/local/lib/python1.5/site-packages/MMTK/ForceFields/MMForceField.py",
line 96, in addBondTerm
raise KeyError, 'No parameters for bond ' + `a1` + '--' + `a2`
KeyError: No parameters for bond Atom bcdex3.C1--Atom bcdex3.C2
>>>
Why??.. my bcdex molecule works well in MMTK last version ..
Maybe is because the opls_atom_type and opls_charge missing..
Explain me please..
This is my bcdex molecule
name = 'bcdex3'
C1 = Atom('C')
C2 = Atom('C')
C3 = Atom('C')
C4 = Atom('C')
O5 = Atom('O')
C6 = Atom('C')
C7 = Atom('C')
C8 = Atom('C')
C9 = Atom('C')
O10 = Atom('O')
C11 = Atom('C')
C12 = Atom('C')
C13 = Atom('C')
C14 = Atom('C')
O15 = Atom('O')
C16 = Atom('C')
C17 = Atom('C')
C18 = Atom('C')
O19 = Atom('O')
O20 = Atom('O')
O21 = Atom('O')
C22 = Atom('C')
C23 = Atom('C')
O24 = Atom('O')
O25 = Atom('O')
O26 = Atom('O')
O27 = Atom('O')
C28 = Atom('C')
C29 = Atom('C')
O30 = Atom('O')
O31 = Atom('O')
O32 = Atom('O')
O33 = Atom('O')
C34 = Atom('C')
C35 = Atom('C')
O36 = Atom('O')
O37 = Atom('O')
O38 = Atom('O')
O39 = Atom('O')
C40 = Atom('C')
C41 = Atom('C')
O42 = Atom('O')
O43 = Atom('O')
C44 = Atom('C')
C45 = Atom('C')
C46 = Atom('C')
C47 = Atom('C')
O48 = Atom('O')
C49 = Atom('C')
C50 = Atom('C')
C51 = Atom('C')
C52 = Atom('C')
O53 = Atom('O')
C54 = Atom('C')
C55 = Atom('C')
C56 = Atom('C')
C57 = Atom('C')
O58 = Atom('O')
C59 = Atom('C')
O60 = Atom('O')
O61 = Atom('O')
C62 = Atom('C')
C63 = Atom('C')
O64 = Atom('O')
O65 = Atom('O')
O66 = Atom('O')
O67 = Atom('O')
C68 = Atom('C')
C69 = Atom('C')
O70 = Atom('O')
O71 = Atom('O')
O72 = Atom('O')
O73 = Atom('O')
C74 = Atom('C')
C75 = Atom('C')
O76 = Atom('O')
O77 = Atom('O')
H78 = Atom('H')
H79 = Atom('H')
H80 = Atom('H')
H81 = Atom('H')
H82 = Atom('H')
H83 = Atom('H')
H84 = Atom('H')
H85 = Atom('H')
H86 = Atom('H')
H87 = Atom('H')
H88 = Atom('H')
H89 = Atom('H')
H90 = Atom('H')
H91 = Atom('H')
H92 = Atom('H')
H93 = Atom('H')
H94 = Atom('H')
H95 = Atom('H')
H96 = Atom('H')
H97 = Atom('H')
H98 = Atom('H')
H99 = Atom('H')
H100 = Atom('H')
H101 = Atom('H')
H102 = Atom('H')
H103 = Atom('H')
H104 = Atom('H')
H105 = Atom('H')
H106 = Atom('H')
H107 = Atom('H')
H108 = Atom('H')
H109 = Atom('H')
H110 = Atom('H')
H111 = Atom('H')
H112 = Atom('H')
H113 = Atom('H')
H114 = Atom('H')
H115 = Atom('H')
H116 = Atom('H')
H117 = Atom('H')
H118 = Atom('H')
H119 = Atom('H')
H120 = Atom('H')
H121 = Atom('H')
H122 = Atom('H')
H123 = Atom('H')
H124 = Atom('H')
H125 = Atom('H')
H126 = Atom('H')
H127 = Atom('H')
H128 = Atom('H')
H129 = Atom('H')
H130 = Atom('H')
H131 = Atom('H')
H132 = Atom('H')
H133 = Atom('H')
H134 = Atom('H')
H135 = Atom('H')
H136 = Atom('H')
H137 = Atom('H')
H138 = Atom('H')
H139 = Atom('H')
H140 = Atom('H')
H141 = Atom('H')
H142 = Atom('H')
H143 = Atom('H')
H144 = Atom('H')
H145 = Atom('H')
H146 = Atom('H')
H147 = Atom('H')
bonds = [Bond(C2, C1), Bond(C3, C2), Bond(C4, C3), Bond(O5, C4),
Bond(C6, O5), Bond(C7, C6), Bond(C8, C7), Bond(C9, C8),
Bond(O10, C9), Bond(C11, O10), Bond(C12, C11), Bond(C13, C12),
Bond(C14, C13), Bond(O15, C14), Bond(C16, O15), Bond(C17, C16),
Bond(C18, C17), Bond(C18, C59), Bond(O19, C18), Bond(O20, C17),
Bond(O21, C16),
Bond(C22, O21), Bond(C22, C59), Bond(C23, C22), Bond(O24, C23),
Bond(O25, C13),
Bond(O26, C12), Bond(O27, C11), Bond(C28, O27), Bond(C28, C14),
Bond(C29, C28),
Bond(O30, C29), Bond(O31, C8), Bond(O32, C7), Bond(O33, C6),
Bond(C34, C9), Bond(C34, O33), Bond(C35, C34), Bond(O36, C35), Bond(O37,
C3),
Bond(O38, C2), Bond(O39, C1), Bond(C40, C4), Bond(C40, O39), Bond(C41,
C40),
Bond(O42, C41), Bond(O43, C1), Bond(C44, O43), Bond(C45, C44),
Bond(C46, C45), Bond(C47, C46), Bond(O48, C47), Bond(C49, O48),
Bond(C50, C49), Bond(C51, C50), Bond(C52, C51), Bond(O53, C52),
Bond(C54, O53), Bond(C55, C54), Bond(C56, C55), Bond(C57, C56),
Bond(C57, O65),
Bond(O58, C57), Bond(C59, O58), Bond(O60, C56), Bond(O61, C55),
Bond(C62, C54), Bond(C63, C62), Bond(O64, C63), Bond(O65, C62),
Bond(O66, C51), Bond(O67, C50), Bond(C68, C49), Bond(C68, O71),
Bond(C69, C68),
Bond(O70, C69), Bond(O71, C52), Bond(O72, C46), Bond(O73, C45),
Bond(C74, C44), Bond(C74, O77), Bond(C75, C74), Bond(O76, C75),
Bond(O77, C47),
Bond(H78, O19), Bond(H79, C18), Bond(H80, O20), Bond(H81, C17),
Bond(H82, O24), Bond(H83, C23), Bond(H84, C23), Bond(H85, C22),
Bond(H86, C16), Bond(H87, C14), Bond(H88, O25), Bond(H89, C13),
Bond(H90, O26), Bond(H91, C12), Bond(H92, O30), Bond(H93, C29),
Bond(H94, C29), Bond(H95, C28), Bond(H96, C11), Bond(H97, C9),
Bond(H98, O31), Bond(H99, C8), Bond(H100, O32), Bond(H101, C7),
Bond(H102, O36), Bond(H103, C35), Bond(H104, C35), Bond(H105,
C34),
Bond(H106, C6), Bond(H107, C4), Bond(H108, O37), Bond(H109, C3),
Bond(H110, O38), Bond(H111, C2), Bond(H112, O42), Bond(H113, C41),
Bond(H114, C41), Bond(H115, C40), Bond(H116, C59), Bond(H117, C57),
Bond(H118, O60), Bond(H119, C56), Bond(H120, O61), Bond(H121, C55),
Bond(H122, O64), Bond(H123, C63), Bond(H124, C63), Bond(H125, C62),
Bond(H126, C54), Bond(H127, C52), Bond(H128, O66), Bond(H129, C51),
Bond(H130, O67), Bond(H131, C50), Bond(H132, O70), Bond(H133, C69),
Bond(H134, C69), Bond(H135, C68), Bond(H136, C49), Bond(H137, C47),
Bond(H138, O72), Bond(H139, C46), Bond(H140, O73), Bond(H141,
C45),
Bond(H142, O76), Bond(H143, C75), Bond(H144, C75), Bond(H145, C74),
Bond(H146, C44), Bond(H147, C1)]
pdbmap = [('BCD', {'C1': C1,
'C2': C2,
'C3': C3,
'C4': C4,
'O5': O5,
'C6': C6,
'C7': C7,
'C8': C8,
'C9': C9,
'O10': O10,
'C11': C11,
'C12': C12,
'C13': C13,
'C14': C14,
'O15': O15,
'C16': C16,
'C17': C17,
'C18': C18,
'O19': O19,
'O20': O20,
'O21': O21,
'C22': C22,
'C23': C23,
'O24': O24,
'O25': O25,
'O26': O26,
'O27': O27,
'C28': C28,
'C29': C29,
'O30': O30,
'O31': O31,
'O32': O32,
'O33': O33,
'C34': C34,
'C35': C35,
'O36': O36,
'O37': O37,
'O38': O38,
'O39': O39,
'C40': C40,
'C41': C41,
'O42': O42,
'O43': O43,
'C44': C44,
'C45': C45,
'C46': C46,
'C47': C47,
'O48': O48,
'C49': C49,
'C50': C50,
'C51': C51,
'C52': C52,
'O53': O53,
'C54': C54,
'C55': C55,
'C56': C56,
'C57': C57,
'O58': O58,
'C59': C59,
'O60': O60,
'O61': O61,
'C62': C62,
'C63': C63,
'O64': O64,
'O65': O65,
'O66': O66,
'O67': O67,
'C68': C68,
'C69': C69,
'O70': O70,
'O71': O71,
'O72': O72,
'O73': O73,
'C74': C74,
'C75': C75,
'O76': O76,
'O77': O77,
'H78': H78,
'H79': H79,
'H80': H80,
'H81': H81,
'H82': H82,
'H83': H83,
'H84': H84,
'H85': H85,
'H86': H86,
'H87': H87,
'H88': H88,
'H89': H89,
'H90': H90,
'H91': H91,
'H92': H92,
'H93': H93,
'H94': H94,
'H95': H95,
'H96': H96,
'H97': H97,
'H98': H98,
'H99': H99,
'H100': H100,
'H101': H101,
'H102': H102,
'H103': H103,
'H104': H104,
'H105': H105,
'H106': H106,
'H107': H107,
'H108': H108,
'H109': H109,
'H110': H110,
'H111': H111,
'H112': H112,
'H113': H113,
'H114': H114,
'H115': H115,
'H116': H116,
'H117': H117,
'H118': H118,
'H119': H119,
'H120': H120,
'H121': H121,
'H122': H122,
'H123': H123,
'H124': H124,
'H125': H125,
'H126': H126,
'H127': H127,
'H128': H128,
'H129': H129,
'H130': H130,
'H131': H131,
'H132': H132,
'H133': H133,
'H134': H134,
'H135': H135,
'H136': H136,
'H137': H137,
'H138': H138,
'H139': H139,
'H140': H140,
'H141': H141,
'H142': H142,
'H143': H143,
'H144': H144,
'H145': H145,
'H146': H146,
'H147': H147})]
# Just anything, to make the test code work...
amber_atom_type = {C1: 'EC',
C2: 'CT',
C3: 'CT',
C4: 'CT',
O5: 'OG',
C6: 'EC',
C7: 'CT',
C8: 'CT',
C9: 'CT',
O10: 'OG',
C11: 'EC',
C12: 'CT',
C13: 'CT',
C14: 'CT',
O15: 'OG',
C16: 'EC',
C17: 'CT',
C18: 'CT',
O19: 'OH',
O20: 'OH',
O21: 'OS',
C22: 'CT',
C23: 'CT',
O24: 'OH',
O25: 'OH',
O26: 'OH',
O27: 'OS',
C28: 'CT',
C29: 'CT',
O30: 'OH',
O31: 'OH',
O32: 'OH',
O33: 'OS',
C34: 'CT',
C35: 'CT',
O36: 'OH',
O37: 'OH',
O38: 'OH',
O39: 'OS',
C40: 'CT',
C41: 'CT',
O42: 'OH',
O43: 'OG',
C44: 'CT',
C45: 'CT',
C46: 'CT',
C47: 'EC',
O48: 'OG',
C49: 'CT',
C50: 'CT',
C51: 'CT',
C52: 'EC',
O53: 'OG',
C54: 'CT',
C55: 'CT',
C56: 'CT',
C57: 'EC',
O58: 'OG',
C59: 'CT',
O60: 'OH',
O61: 'OH',
C62: 'CT',
C63: 'CT',
O64: 'OH',
O65: 'OS',
O66: 'OH',
O67: 'OH',
C68: 'CT',
C69: 'CT',
O70: 'OH',
O71: 'OS',
O72: 'OH',
O73: 'OH',
C74: 'CT',
C75: 'CT',
O76: 'OH',
O77: 'OS',
H78: 'HO',
H79: 'HC',
H80: 'HO',
H81: 'HC',
H82: 'HO',
H83: 'HC',
H84: 'HC',
H85: 'HC',
H86: 'HC',
H87: 'HC',
H88: 'HO',
H89: 'HC',
H90: 'HO',
H91: 'HC',
H92: 'HO',
H93: 'HC',
H94: 'HC',
H95: 'HC',
H96: 'HC',
H97: 'HC',
H98: 'HO',
H99: 'HC',
H100: 'HO',
H101: 'HC',
H102: 'HO',
H103: 'HC',
H104: 'HC',
H105: 'HC',
H106: 'HC',
H107: 'HC',
H108: 'HO',
H109: 'HC',
H110: 'HO',
H111: 'HC',
H112: 'HO',
H113: 'HC',
H114: 'HC',
H115: 'HC',
H116: 'HC',
H117: 'HC',
H118: 'HO',
H119: 'HC',
H120: 'HO',
H121: 'HC',
H122: 'HO',
H123: 'HC',
H124: 'HC',
H125: 'HC',
H126: 'HC',
H127: 'HC',
H128: 'HO',
H129: 'HC',
H130: 'HO',
H131: 'HC',
H132: 'HO',
H133: 'HC',
H134: 'HC',
H135: 'HC',
H136: 'HC',
H137: 'HC',
H138: 'HO',
H139: 'HC',
H140: 'HO',
H141: 'HC',
H142: 'HO',
H143: 'HC',
H144: 'HC',
H145: 'HC',
H146: 'HC',
H147: 'HC'}
# ¿Porque no funciona?
amber_charge = {C1: 0.364214,
C2: 0.057186,
C3: 0.247514,
C4: 0.117374,
O5: -0.541429,
C6: 0.364214,
C7: 0.057186,
C8: 0.247514,
C9: 0.117374,
O10: -0.541429,
C11: 0.364214,
C12: 0.057186,
C13: 0.247514,
C14: 0.117374,
O15: -0.541429,
C16: 0.364214,
C17: 0.057186,
C18: 0.247514,
O19: -0.586900,
O20: -0.528718,
O21: -0.427929,
C22: 0.050600,
C23: 0.2726770,
O24: -0.5666340,
O25: -0.586900,
O26: -0.528718,
O27: -0.427929,
C28: 0.050600,
C29: 0.2726770,
O30: -0.5666340,
O31: -0.586900,
O32: -0.528718,
O33: -0.427929,
C34: 0.050600,
C35: 0.2726770,
O36: -0.5666340,
O37: -0.586900,
O38: -0.528718,
O39: -0.427929,
C40: 0.050600,
C41: 0.2726770,
O42: -0.5666340,
O43: -0.541429,
C44: 0.117374,
C45: 0.247514,
C46: 0.057186,
C47: 0.364214,
O48: -0.541429,
C49: 0.117374,
C50: 0.247514,
C51: 0.057186,
C52: 0.364214,
O53: -0.541429,
C54: 0.117374,
C55: 0.247514,
C56: 0.057186,
C57: 0.364214,
O58: -0.541429,
C59: 0.117374,
O60: -0.528718,
O61: -0.586900,
C62: 0.050600,
C63: 0.2726770,
O64: -0.5666340,
O65: -0.427929,
O66: -0.528718,
O67: -0.586900,
C68: 0.050600,
C69: 0.2726770,
O70: -0.5666340,
O71: -0.427929,
O72: -0.528718,
O73: -0.586900,
C74: 0.050600,
C75: 0.2726770,
O76: -0.5666340,
O77: -0.427929,
H78: 0.338302,
H79: 0.078928,
H80: 0.349474,
H81: -0.054398,
H82: 0.327934,
H83: 0.018566,
H84: 0.014623,
H85: 0.071536,
H86: 0.080983,
H87: 0.066897,
H88: 0.338302,
H89: 0.078928,
H90: 0.349474,
H91: -0.054398,
H92: 0.327934,
H93: 0.018566,
H94: 0.014623,
H95: 0.071536,
H96: 0.080983,
H97: 0.066897,
H98: 0.338302,
H99: 0.078928,
H100: 0.349474,
H101: -0.054398,
H102: 0.327934,
H103: 0.014623,
H104: 0.018566,
H105: 0.071536,
H106: 0.080983,
H107: 0.066897,
H108: 0.338302,
H109: 0.078928,
H110: 0.349474,
H111: -0.054398,
H112: 0.327934,
H113: 0.018566,
H114: 0.014623,
H115: 0.071536,
H116: 0.066897,
H117: 0.080983,
H118: 0.349474,
H119: -0.054398,
H120: 0.338302,
H121: 0.078928,
H122: 0.327934,
H123: 0.014623,
H124: 0.018566,
H125: 0.071536,
H126: 0.066897,
H127: 0.080983,
H128: 0.349474,
H129: -0.054398,
H130: 0.338302,
H131: 0.078928,
H132: 0.327934,
H133: 0.014623,
H134: 0.018566,
H135: 0.071536,
H136: 0.066897,
H137: 0.080983,
H138: 0.349474,
H139: -0.054398,
H140: 0.338302,
H141: 0.078928,
H142: 0.327934,
H143: 0.014623,
H144: 0.018566,
H145: 0.071536,
H146: 0.066897,
H147: 0.080983}
configurations = {
'default': PDBFile('bcdex3.pdb')
}
Please help me..
Tanks
Julio =)
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