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Copy pathmartinize2.6_lipidtails.py
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martinize2.6_lipidtails.py
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#!/usr/bin/env python
# EDITABLE SECTIONS ARE MARKED WITH #@#
version = "2.6"
authors = ["Djurre H. de Jong", "Jaakko J. Uusitalo", "Tsjerk A. Wassenaar"]
'Updated with lipid tail parameters according to DOI:10.1021/acs.jpcb.7b10175 - Dheeraj Prakaash (DJ) - 2nd Oct 2019'
'Modifications / newly added lines are followed by "# DJ" in this script'
'Atom names of lipidated residues were obtained from CHARMM GUI'
'Myristoylation only on N-terminal GLY (CHARMM-GUI mutates any N-terminus residue to GLY automatically before adding myristoyl group)'
'GMN here refers to GYM in DOI:10.1021/acs.jpcb.7b10175'
# This program has grown to be pretty complex.
# The routines have been organized in different files.
# For working versions, all files can be incorporated by using the catenate.py file.
#
# Index of the program files:
#
# 1. Options and documentation @DOC.py
# 2. Description, options and command line parsing @CMD.py
# 3. Helper functions and macros @FUNC.py
# 4. Finegrained to coarsegrained mapping @MAP.py
# 5. Secondary structure determination and interpretation @SS.py
# 6. Elastic network @ELN.py
# 7. Structure I/O @IO.py
# 8. Topology generation @TOP.py
# 9. Main @MAIN.py
#
# Force field parameters are specified in the differentt forcefield modules,
# e.g.: martini22_ff.py
################################
## 6 # FORCE FIELD PARAMETERS ## -> @FF <-
################################
class martini21:
ff = True
def __init__(self):
# parameters are defined here for the following (protein) forcefields:
self.name = 'martini21'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"),# ALA specific #@#
"PRO": spl(" C5 N0 C5 N0 Na N0 N0 Na Na"),# PRO specific #@#
"HYP": spl(" C5 N0 C5 N0 N0 N0 N0 Na Na") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .350, .350, .350, .350, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, 1250, 1250, 1250, 1250, 500, 400, 400) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = ( 119.2,134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 25, 25, 25) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = ( 90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
# martini 2.1 doesn't
self.ca2bb = False
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# To be compatible with Elnedyn, all parameters are explicitly defined, even if they are double.
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"TRP": [spl("SC4 SP1 SC4 SC4"),[(0.300,5000)]+[(0.270,None) for i in range(5)], [(210,50),(90,50),(90,50)], [(0,50),(0,200)]],
"TYR": [spl("SC4 SC4 SP1"), [(0.320,5000), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"PHE": [spl("SC4 SC4 SC4"), [(0.310,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIS": [spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIH": [spl("SC4 SP1 SQd"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"ARG": [spl("N0 Qd"), [(0.330,5000), (0.340,5000)], [(180,25)]],
"LYS": [spl("C3 Qd"), [(0.330,5000), (0.280,5000)], [(180,25)]],
"CYS": [spl("C5"), [(0.310,7500)]],
"ASP": [spl("Qa"), [(0.320,7500)]],
"GLU": [spl("Qa"), [(0.400,5000)]],
"ILE": [spl("AC1"), [(0.310,None)]],
"LEU": [spl("AC1"), [(0.330,7500)]],
"MET": [spl("C5"), [(0.400,2500)]],
"ASN": [spl("P5"), [(0.320,5000)]],
"PRO": [spl("AC2"), [(0.300,7500)]],
"HYP": [spl("P1"), [(0.300,7500)]],
"GLN": [spl("P4"), [(0.400,5000)]],
"SER": [spl("P1"), [(0.250,7500)]],
"THR": [spl("P1"), [(0.260,None)]],
"VAL": [spl("AC2"), [(0.265,None)]],
"ALA": [],
"GLY": [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = True
self.UseBBBBDihedrals = True
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = []
self.charged = []
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
}
# Defines the connectivity between between beads
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0,1),(1,2),(1,3),(2,3),(2,4),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1),(1,2,4,3)]],
"TYR": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"PHE": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIS": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIH": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"GLN": [[(0,1)]],
"ASN": [[(0,1)]],
"SER": [[(0,1)]],
"THR": [[(0,1)]],
"ARG": [[(0,1),(1,2)], [(0,1,2)]],
"LYS": [[(0,1),(1,2)], [(0,1,2)]],
"ASP": [[(0,1)]],
"GLU": [[(0,1)]],
"CYS": [[(0,1)]],
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = False
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 6
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = hash(bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i,hash(bbss,self.bbtyp[i])) for i in self.bbtyp.keys()])
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = hash(bbss,zip(self.bbldef,self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([(i,hash(bbss,zip(self.bbltyp[i],self.bbkbtyp[i]))) for i in self.bbltyp.keys()])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = hash(bbss,zip(self.bbadef,self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([(i,hash(bbss,zip(self.bbatyp[i],self.bbkatyp[i]))) for i in self.bbatyp.keys()])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = hash(bbss,zip(self.bbddef,self.bbkd,self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([(i,hash(bbss,zip(self.bbdtyp[i],self.bbkdtyp[i]))) for i in self.bbdtyp.keys()])
# The following function returns the backbone bead for a given residue and
# secondary structure type.
# 1. Look up the proper dictionary for the residue
# 2. Get the proper type from it for the secondary structure
# If the residue is not in the dictionary of specials, use the default
# If the secondary structure is not listed (in the residue specific
# dictionary) revert to the default.
def bbGetBead(self,r1,ss="C"):
return self.bbBeadDictS.get(r1,self.bbBeadDictD).get(ss,self.bbBeadDictD.get(ss))
def bbGetBond(self,r,a,ss):
# Retrieve parameters for each residue from table defined above
b1 = self.bbBondDictS.get(r[0],self.bbBondDictD).get(ss[0],self.bbBondDictD.get(ss[0]))
b2 = self.bbBondDictS.get(r[1],self.bbBondDictD).get(ss[1],self.bbBondDictD.get(ss[1]))
# Determine which parameters to use for the bond
return ( (b1[0]+b2[0])/2, min(b1[1],b2[1]) )
def bbGetAngle(self,r,ca,ss):
# PRO in helices is dominant
if r[1] == "PRO" and ss[1] in "H123":
return self.bbAngleDictS["PRO"].get(ss[1])
else:
# Retrieve parameters for each residue from table defined above
a = [ self.bbAngleDictS.get(r[0],self.bbAngleDictD).get(ss[0],self.bbAngleDictD.get(ss[0])),
self.bbAngleDictS.get(r[1],self.bbAngleDictD).get(ss[1],self.bbAngleDictD.get(ss[1])),
self.bbAngleDictS.get(r[2],self.bbAngleDictD).get(ss[2],self.bbAngleDictD.get(ss[2])) ]
# Sort according to force constant
a.sort(key=lambda i: (i[1],i[0]))
# This selects the set with the smallest force constant and the smallest angle
return a[0]
def messages(self):
import logging
'''Prints any force-field specific logging messages.'''
logging.info('Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.')
################################
## 6 # FORCE FIELD PARAMETERS ## -> @FF <-
################################
class martini21p:
ff = True
def __init__(self):
# parameters are defined here for the following (protein) forcefields:
self.name = 'martini21p'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"),# ALA specific #@#
"PRO": spl(" C5 N0 C5 N0 Na N0 N0 Na Na"),# PRO specific #@#
"HYP": spl(" C5 N0 C5 N0 N0 N0 N0 Na Na") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .350, .350, .350, .350, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, 1250, 1250, 1250, 1250, 500, 400, 400) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = ( 119.2,134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 25, 25, 25) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = ( 90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
# martini 2.1 doesn't
self.ca2bb = False
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# To be compatible with Elnedyn, all parameters are explicitly defined, even if they are double.
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"TRP": [spl("SC4 SP1 SC4 SC4"),[(0.300,5000)]+[(0.270,None) for i in range(5)], [(210,50),(90,50),(90,50)], [(0,50),(0,200)]],
"TYR": [spl("SC4 SC4 SP1"), [(0.320,5000), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"PHE": [spl("SC4 SC4 SC4"), [(0.310,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIS": [spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIH": [spl("SC4 SP1 SQd"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"ARG": [spl("N0 Qd"), [(0.330,5000), (0.340,5000)], [(180,25)]],
"LYS": [spl("C3 Qd"), [(0.330,5000), (0.280,5000)], [(180,25)]],
"CYS": [spl("C5"), [(0.310,7500)]],
"ASP": [spl("Qa"), [(0.320,7500)]],
"GLU": [spl("Qa"), [(0.400,5000)]],
"ILE": [spl("C1"), [(0.310,None)]],
"LEU": [spl("C1"), [(0.330,7500)]],
"MET": [spl("C5"), [(0.400,2500)]],
"ASN": [spl("P5"), [(0.320,5000)]],
"PRO": [spl("C2"), [(0.300,7500)]],
"HYP": [spl("P1"), [(0.300,7500)]],
"GLN": [spl("P4"), [(0.400,5000)]],
"SER": [spl("P1"), [(0.250,7500)]],
"THR": [spl("P1"), [(0.260,None)]],
"VAL": [spl("C2"), [(0.265,None)]],
"ALA": [],
"GLY": [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = True
self.UseBBBBDihedrals = True
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = []
self.charged = []
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
}
# Defines the connectivity between between beads
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0,1),(1,2),(1,3),(2,3),(2,4),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1),(1,2,4,3)]],
"TYR": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"PHE": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIS": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIH": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"GLN": [[(0,1)]],
"ASN": [[(0,1)]],
"SER": [[(0,1)]],
"THR": [[(0,1)]],
"ARG": [[(0,1),(1,2)], [(0,1,2)]],
"LYS": [[(0,1),(1,2)], [(0,1,2)]],
"ASP": [[(0,1)]],
"GLU": [[(0,1)]],
"CYS": [[(0,1)]],
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = False
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 6
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = hash(bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i,hash(bbss,self.bbtyp[i])) for i in self.bbtyp.keys()])
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = hash(bbss,zip(self.bbldef,self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([(i,hash(bbss,zip(self.bbltyp[i],self.bbkbtyp[i]))) for i in self.bbltyp.keys()])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = hash(bbss,zip(self.bbadef,self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([(i,hash(bbss,zip(self.bbatyp[i],self.bbkatyp[i]))) for i in self.bbatyp.keys()])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = hash(bbss,zip(self.bbddef,self.bbkd,self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([(i,hash(bbss,zip(self.bbdtyp[i],self.bbkdtyp[i]))) for i in self.bbdtyp.keys()])
# The following function returns the backbone bead for a given residue and
# secondary structure type.
# 1. Look up the proper dictionary for the residue
# 2. Get the proper type from it for the secondary structure
# If the residue is not in the dictionary of specials, use the default
# If the secondary structure is not listed (in the residue specific
# dictionary) revert to the default.
def bbGetBead(self,r1,ss="C"):
return self.bbBeadDictS.get(r1,self.bbBeadDictD).get(ss,self.bbBeadDictD.get(ss))
def bbGetBond(self,r,a,ss):
# Retrieve parameters for each residue from table defined above
b1 = self.bbBondDictS.get(r[0],self.bbBondDictD).get(ss[0],self.bbBondDictD.get(ss[0]))
b2 = self.bbBondDictS.get(r[1],self.bbBondDictD).get(ss[1],self.bbBondDictD.get(ss[1]))
# Determine which parameters to use for the bond
return ( (b1[0]+b2[0])/2, min(b1[1],b2[1]) )
def bbGetAngle(self,r,ca,ss):
# PRO in helices is dominant
if r[1] == "PRO" and ss[1] in "H123":
return self.bbAngleDictS["PRO"].get(ss[1])
else:
# Retrieve parameters for each residue from table defined above
a = [ self.bbAngleDictS.get(r[0],self.bbAngleDictD).get(ss[0],self.bbAngleDictD.get(ss[0])),
self.bbAngleDictS.get(r[1],self.bbAngleDictD).get(ss[1],self.bbAngleDictD.get(ss[1])),
self.bbAngleDictS.get(r[2],self.bbAngleDictD).get(ss[2],self.bbAngleDictD.get(ss[2])) ]
# Sort according to force constant
a.sort(key=lambda i: (i[1],i[0]))
# This selects the set with the smallest force constant and the smallest angle
return a[0]
def messages(self):
'''Prints any force-field specific logging messages.'''
logging.info('Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.')
################################
## 6 # FORCE FIELD PARAMETERS ## -> @FF <-
################################
# New martini 2.2 parameters.
# Changed:
# Unstructured Pro backbone bead
# Proline side chains
# Phe sidechain
# Trp sidechain
# Helix BB-bonds to constraint
class martini22:
ff = True
def __init__(self):
# parameters are defined here for the following (protein) forcefields:
self.name = 'martini22'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"), # ALA specific #@#
"PRO": spl(" C5 N0 C5 N0 Na N0 N0 P4 P4"), # PRO specific #@#
"HYP": spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .310, .310, .310, .310, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, None, None, None, None, 1250, 1250, 1250) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = ( 119.2,134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 20, 20, 20) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = ( 90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
# martini 2.1 doesn't
self.ca2bb = False
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# To be compatible with Elnedyn, all parameters are explicitly defined, even if they are double.
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"TRP": [spl("SC4 SNd SC5 SC5"), [(0.300,5000)]+[(0.270,None) for i in range(5)], [(210,50),(90,50),(90,50)], [(0,50),(0,200)]],
"TYR": [spl("SC4 SC4 SP1"), [(0.320,5000), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"PHE": [spl("SC5 SC5 SC5"), [(0.310,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIS": [spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"HIH": [spl("SC4 SP1 SQd"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)],[(150,50),(150,50)], [(0,50)]],
"ARG": [spl("N0 Qd"), [(0.330,5000), (0.340,5000)], [(180,25)]],
"LYS": [spl("C3 Qd"), [(0.330,5000), (0.280,5000)], [(180,25)]],
"CYS": [spl("C5"), [(0.310,7500)]], # ANGLES (No dihedrals for lipid tails)
"CYF": [spl("C5 C3 C3 C3 C3"), [(0.390,8000)]+[(0.420,6000),(0.430,5000),(0.31,12000),(0.23,15000)], [(180,65),(125,42),(130,48),(170,50)]], # DJ
"CYG": [spl("C5 C3 C3 C3 C3 C3"),[(0.380,8500)]+[(0.420,6000),(0.420,7750),(0.410,7000),(0.400,9000),(0.240,8000)], [(150,50),(125,55),(130,45),(180,38),(180,75)]], # DJ
"CYP": [spl("C5 C1 C1 C1 C1"), [(0.380,8000)]+[(0.390,5000),(0.470,4500),(0.470,4500),(0.410,5500)], [(150,35),(125,25),(180,25),(180,28)]], # DJ
"GMN": [spl("C1 C1 C1 C1"), [(0.360,7500)]+[(0.470,3000),(0.470,4000),(0.360,5000)], [(140,30),(160,38),(175,45)]], # DJ
"ASP": [spl("Qa"), [(0.320,7500)]],
"GLU": [spl("Qa"), [(0.400,5000)]],
"ILE": [spl("AC1"), [(0.310,None)]],
"LEU": [spl("AC1"), [(0.330,7500)]],
"MET": [spl("C5"), [(0.400,2500)]],
"ASN": [spl("P5"), [(0.320,5000)]],
"PRO": [spl("C3"), [(0.300,7500)]],
"HYP": [spl("P1"), [(0.300,7500)]],
"GLN": [spl("P4"), [(0.400,5000)]],
"SER": [spl("P1"), [(0.250,7500)]],
"THR": [spl("P1"), [(0.260,None)]],
"VAL": [spl("AC2"), [(0.265,None)]],
"ALA": [],
"GLY": [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = True
self.UseBBBBDihedrals = True
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = []
self.charged = []
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
}
# Defines the connectivity between between beads
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0,1),(1,2),(1,3),(2,3),(2,4),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1),(1,2,4,3)]],
"TYR": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"PHE": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIS": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIH": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"GLN": [[(0,1)]],
"ASN": [[(0,1)]],
"SER": [[(0,1)]],
"THR": [[(0,1)]],
"ARG": [[(0,1),(1,2)], [(0,1,2)]],
"LYS": [[(0,1),(1,2)], [(0,1,2)]],
"ASP": [[(0,1)]],
"GLU": [[(0,1)]],
"CYS": [[(0,1)]],
"CYF": [[(0,1),(1,2),(2,3),(3,4),(4,5)], [(0,1,2),(1,2,3),(2,3,4),(3,4,5)]], # DJ
"CYG": [[(0,1),(1,2),(2,3),(3,4),(4,5),(5,6)], [(0,1,2),(1,2,3),(2,3,4),(3,4,5),(4,5,6)]], # DJ
"CYP": [[(0,1),(1,2),(2,3),(3,4),(4,5)], [(0,1,2),(1,2,3),(2,3,4),(3,4,5)]], # DJ
"GMN": [[(0,1),(1,2),(2,3),(3,4)], [(0,1,2),(1,2,3),(2,3,4)]], # DJ
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = False
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 6
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = hash(bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)
self.bbBeadDictS = dict([(i,hash(bbss,self.bbtyp[i])) for i in self.bbtyp.keys()])
## BB BOND TYPE ##
# Dictionary of default abond types (*D)
self.bbBondDictD = hash(bbss,zip(self.bbldef,self.bbkb))
# Dictionary of dictionaries for specific types (*S)
self.bbBondDictS = dict([(i,hash(bbss,zip(self.bbltyp[i],self.bbkbtyp[i]))) for i in self.bbltyp.keys()])
# This is tricky to read, but it gives the right bondlength/force constant
## BBB ANGLE TYPE ##
# Dictionary of default angle types (*D)
self.bbAngleDictD = hash(bbss,zip(self.bbadef,self.bbka))
# Dictionary of dictionaries for specific types (*S)
self.bbAngleDictS = dict([(i,hash(bbss,zip(self.bbatyp[i],self.bbkatyp[i]))) for i in self.bbatyp.keys()])
## BBBB DIHEDRAL TYPE ##
# Dictionary of default dihedral types (*D)
self.bbDihedDictD = hash(bbss,zip(self.bbddef,self.bbkd,self.bbdmul))
# Dictionary of dictionaries for specific types (*S)
self.bbDihedDictS = dict([(i,hash(bbss,zip(self.bbdtyp[i],self.bbkdtyp[i]))) for i in self.bbdtyp.keys()])
# The following function returns the backbone bead for a given residue and
# secondary structure type.
# 1. Look up the proper dictionary for the residue
# 2. Get the proper type from it for the secondary structure
# If the residue is not in the dictionary of specials, use the default
# If the secondary structure is not listed (in the residue specific
# dictionary) revert to the default.
def bbGetBead(self,r1,ss="C"):
return self.bbBeadDictS.get(r1,self.bbBeadDictD).get(ss,self.bbBeadDictD.get(ss))
def bbGetBond(self,r,a,ss):
# Retrieve parameters for each residue from table defined above
b1 = self.bbBondDictS.get(r[0],self.bbBondDictD).get(ss[0],self.bbBondDictD.get(ss[0]))
b2 = self.bbBondDictS.get(r[1],self.bbBondDictD).get(ss[1],self.bbBondDictD.get(ss[1]))
# Determine which parameters to use for the bond
return ( (b1[0]+b2[0])/2, min(b1[1],b2[1]) )
def bbGetAngle(self,r,ca,ss):
# PRO in helices is dominant
if r[1] == "PRO" and ss[1] in "H123":
return self.bbAngleDictS["PRO"].get(ss[1])
else:
# Retrieve parameters for each residue from table defined above
a = [ self.bbAngleDictS.get(r[0],self.bbAngleDictD).get(ss[0],self.bbAngleDictD.get(ss[0])),
self.bbAngleDictS.get(r[1],self.bbAngleDictD).get(ss[1],self.bbAngleDictD.get(ss[1])),
self.bbAngleDictS.get(r[2],self.bbAngleDictD).get(ss[2],self.bbAngleDictD.get(ss[2])) ]
# Sort according to force constant
a.sort(key=lambda i: (i[1],i[0]))
# This selects the set with the smallest force constant and the smallest angle
return a[0]
def messages(self):
'''Prints any force-field specific logging messages.'''
import logging
logging.info('Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.')
################################
## 6 # FORCE FIELD PARAMETERS ## -> @FF <-
################################
# New martini 2.2p parameters.
# Changed:
# Unstructured Pro backbone bead
# Proline side chains
# Phe sidechain
# Trp sidechain
# Polar beads
# Helix BB-bonds to constraint
# Todo:
# Helix BB-bond length
class martini22p:
ff = True
def __init__(self):
# parameters are defined here for the following (protein) forcefields:
self.name = 'martini22p'
# Charged types:
self.charges = {"Qd":1, "Qa":-1, "SQd":1, "SQa":-1, "RQd":1, "AQa":-1} #@#
#----+---------------------+
## A | BACKBONE PARAMETERS |
#----+---------------------+
#
# bbss lists the one letter secondary structure code
# bbdef lists the corresponding default backbone beads
# bbtyp lists the corresponding residue specific backbone beads
#
# bbd lists the structure specific backbone bond lengths
# bbkb lists the corresponding bond force constants
#
# bba lists the structure specific angles
# bbka lists the corresponding angle force constants
#
# bbd lists the structure specific dihedral angles
# bbkd lists the corresponding force constants
#
# -=NOTE=-
# if the secondary structure types differ between bonded atoms
# the bond is assigned the lowest corresponding force constant
#
# -=NOTE=-
# if proline is anywhere in the helix, the BBB angle changes for
# all residues
#
###############################################################################################
## BEADS ## #
# F E H 1 2 3 T S C # SS one letter
self.bbdef = spl(" N0 Nda N0 Nd Na Nda Nda P5 P5") # Default beads #@#
self.bbtyp = { # #@#
"ALA": spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4"), # ALA specific #@#
"PRO": spl(" C5 N0 C5 N0 Na N0 N0 P4 P4"), # PRO specific #@#
"HYP": spl(" C5 N0 C5 N0 N0 N0 N0 P4 P4") # HYP specific #@#
} # #@#
## BONDS ## #
self.bbldef = (.365, .350, .310, .310, .310, .310, .350, .350, .350) # BB bond lengths #@#
self.bbkb = (1250, 1250, None, None, None, None, 1250, 1250, 1250) # BB bond kB #@#
self.bbltyp = {} # #@#
self.bbkbtyp = {} # #@#
## ANGLES ## #
self.bbadef = ( 119.2,134, 96, 96, 96, 96, 100, 130, 127) # BBB angles #@#
self.bbka = ( 150, 25, 700, 700, 700, 700, 25, 25, 25) # BBB angle kB #@#
self.bbatyp = { # #@#
"PRO": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127), # PRO specific #@#
"HYP": ( 119.2,134, 98, 98, 98, 98, 100, 130, 127) # PRO specific #@#
} # #@#
self.bbkatyp = { # #@#
"PRO": ( 150, 25, 100, 100, 100, 100, 25, 25, 25), # PRO specific #@#
"HYP": ( 150, 25, 100, 100, 100, 100, 25, 25, 25) # PRO specific #@#
} # #@#
## DIHEDRALS ## #
self.bbddef = ( 90.7, 0, -120, -120, -120, -120) # BBBB dihedrals #@#
self.bbkd = ( 100, 10, 400, 400, 400, 400) # BBBB kB #@#
self.bbdmul = ( 1, 1, 1, 1, 1, 1) # BBBB mltplcty #@#
self.bbdtyp = {} # #@#
self.bbkdtyp = {} # #@#
#
###############################################################################################
# Some Forcefields use the Ca position to position the BB-bead (me like!)
# martini 2.1 doesn't
self.ca2bb = False
# BBS angle, equal for all ss types
# Connects BB(i-1),BB(i),SC(i), except for first residue: BB(i+1),BB(i),SC(i)
# ANGLE Ka
self.bbsangle = [ 100, 25] #@#
# Bonds for extended structures (more stable than using dihedrals)
# LENGTH FORCE
self.ebonds = { #@#
'short': [ .640, 2500], #@#
'long' : [ .970, 2500] #@#
} #@#
#----+-----------------------+
## B | SIDE CHAIN PARAMETERS |
#----+-----------------------+
# To be compatible with Elnedyn, all parameters are explicitly defined, even if they are double.
self.sidechains = {
#RES# BEADS BONDS ANGLES DIHEDRALS V-SITES
# BB-SC SC-SC BB-SC-SC SC-SC-SC
"TRP": [spl("SC4 SNd SC5 SC5"),[(0.300,5000)]+[(0.270,None) for i in range(5)], [(210,50),(90,50),(90,50)], [(0,50),(0,200)]],
"TYR": [spl("SC4 SC4 SP1"), [(0.320,5000), (0.270,None), (0.270,None),(0.270,None)], [(150,50),(150,50)], [(0,50)]],
"PHE": [spl("SC5 SC5 SC5"), [(0.310,7500), (0.270,None), (0.270,None),(0.270,None)], [(150,50),(150,50)], [(0,50)]],
"HIS": [spl("SC4 SP1 SP1"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None)], [(150,50),(150,50)], [(0,50)]],
"HIH": [spl("SC4 SP1 SQd D"), [(0.320,7500), (0.270,None), (0.270,None),(0.270,None),(0.11,None)],[(150,50),(150,50)], [(0,50)]],
"GLN": [spl("Nda D D"), [(0.400,5000), (0.280,None)], [], [], [(0.5,)]],
"ASN": [spl("Nda D D"), [(0.320,5000), (0.280,None)], [], [], [(0.5,)]],
"SER": [spl("N0 D D"), [(0.250,7500), (0.280,None)], [], [], [(0.5,)]],
"THR": [spl("N0 D D"), [(0.260,9000), (0.280,None)], [], [], [(0.5,)]],
"ARG": [spl("N0 Qd D"), [(0.330,5000), (0.340,5000), (0.110,None)], [(180,25)]],
"LYS": [spl("C3 Qd D"), [(0.330,5000), (0.280,5000), (0.110,None)], [(180,25)]],
"ASP": [spl("Qa D"), [(0.320,7500), (0.110,None)]],
"GLU": [spl("Qa D"), [(0.400,5000), (0.110,None)]],
"CYS": [spl("C5"), [(0.310,7500)]],
"ILE": [spl("C1"), [(0.310,None)]],
"LEU": [spl("C1"), [(0.330,7500)]],
"MET": [spl("C5"), [(0.400,2500)]],
"PRO": [spl("C3"), [(0.300,7500)]],
"HYP": [spl("P1"), [(0.300,7500)]],
"VAL": [spl("C2"), [(0.265,None)]],
"ALA": [],
"GLY": [],
}
# Not all (eg Elnedyn) forcefields use backbone-backbone-sidechain angles and BBBB-dihedrals.
self.UseBBSAngles = True
self.UseBBBBDihedrals = True
# Martini 2.2p has polar and charged residues with seperate charges.
self.polar = ["GLN","ASN","SER","THR"]
self.charged = ["ARG","LYS","ASP","GLU","HIH"]
# If masses or charged diverge from standard (45/72 and -/+1) they are defined here.
self.mass_charge = {
#RES MASS CHARGE
"GLN":[[0,36,36], [0,0.42,-0.42]],
"ASN":[[0,36,36], [0,0.46,-0.46]],
"SER":[[0,36,36], [0,0.40,-0.40]],
"THR":[[0,36,36], [0,0.36,-0.36]],
"ARG":[[72,36,36], [0,0,1]],
"LYS":[[72,36,36], [0,0,1]],
"HIH":[[45,45,36,36], [0,0,0,1]],
"ASP":[[36,36], [0,-1]],
"GLU":[[36,36], [0,-1]],
}
self.connectivity = {
#RES BONDS ANGLES DIHEDRALS V-SITE
"TRP": [[(0,1),(1,2),(1,3),(2,3),(2,4),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1),(1,2,4,3)]],
"TYR": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"PHE": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIS": [[(0,1),(1,2),(1,3),(2,3)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"HIH": [[(0,1),(1,2),(1,3),(2,3),(3,4)], [(0,1,2),(0,1,3)], [(0,2,3,1)]],
"GLN": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"ASN": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"SER": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"THR": [[(0,1),(2,3)], [], [], [(1,2,3)]],
"ARG": [[(0,1),(1,2),(2,3)], [(0,1,2)]],
"LYS": [[(0,1),(1,2),(2,3)], [(0,1,2)]],
"ASP": [[(0,1),(1,2)]],
"GLU": [[(0,1),(1,2)]],
"CYS": [[(0,1)]],
"ILE": [[(0,1)]],
"LEU": [[(0,1)]],
"MET": [[(0,1)]],
"PRO": [[(0,1)]],
"HYP": [[(0,1)]],
"VAL": [[(0,1)]],
"ALA": [],
"GLY": [],
}
#----+----------------+
## C | SPECIAL BONDS |
#----+----------------+
self.special = {
# Used for sulfur bridges
# ATOM 1 ATOM 2 BOND LENGTH FORCE CONSTANT
(("SC1","CYS"), ("SC1","CYS")): (0.24, None),
}
# By default use an elastic network
self.ElasticNetwork = False
# Elastic networks bond shouldn't lead to exclusions (type 6)
# But Elnedyn has been parametrized with type 1.
self.EBondType = 6
#----+----------------+
## D | INTERNAL STUFF |
#----+----------------+
## BACKBONE BEAD TYPE ##
# Dictionary of default bead types (*D)
self.bbBeadDictD = hash(bbss,self.bbdef)
# Dictionary of dictionaries of types for specific residues (*S)