[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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