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Merge pull request #68 from ojeda-e/PIP_2021
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Updated 2021 Phosphatidylinositde lipids added to lipid_data
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@Tsjerk
Tsjerk authored Jul 7, 2021
2 parents 362ed5a + b867cdf commit d82d70b
Showing 1 changed file with 42 additions and 1 deletion.
43 changes: 42 additions & 1 deletion insane/_lipid_data.py
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"LPPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A C2A C3A C4A - - C1B C2B C3B - - - "),
"LOPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B - - - "),
"YPPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A C2A C3A C4A - - C1B D2B C3B - - - "),
"POPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
# "POPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "), --> Replace by 2021 22 bead below
"PIPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 C1A D2A D3A C4A - - C1B C2B C3B C4B - - "),
"PAPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 D1A D2A D3A D4A C5A - C1B C2B C3B C4B - - "),
"PUPI": (moltype, " C1 C2 C3 PO4 - - - GL1 GL2 D1A D2A D3A D4A D5A - C1B C2B C3B C4B - - "),
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"PI34.o": (moltype, " C1 C2 C3 CP PO1 PO2 - GL1 GL2 C1A C2A C3A C4A - - CU1 CU2 CU3 CU4 CU5 - "),
})

# 8 6
# \|
# 3 - 1-5-9-11-12-13-14-15 # chain B
# | 4 / |
# | / |
# 7-2 10-16-17-18-19-20 # chain A
moltype = "INOSITIDES"
# From L. Borges-Araujo, P.C.T. Souza, F. Fernandes and M.N. Melo, Improved
# parameterization of phosphatidylinositide lipid head-groups for the Martini 3
# coarse grain force field doi:10.26434/chemrxiv.14759991. Added by ojeda-e 2020.07.06
lipidsx[moltype] = ( .5, .5, 0, 0.75, 0, 1, .5, 0, 0, .5, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
lipidsy[moltype] = ( 0, 0, 0, 0.25, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 8, 9, 9, 8.5, 7, 10, 10, 10, 6, 6, 5, 4, 3, 2, 1, 5, 4, 3, 2, 1, 0)
lipidsa.update({ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
"SAPI" : (moltype, " C1 C2 C3 C4 PO4 - - - GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"SAP1_3" : (moltype, " C1 C2 C3 C4 PO4 P3 - - GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"SAP1_4" : (moltype, " C1 C2 C3 C4 PO4 - - P4 GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"SAP1_5" : (moltype, " C1 C2 C3 C4 PO4 - P5 - GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"SAP2_34" : (moltype, " C1 C2 C3 C4 PO4 P3 - P4 GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"SAP2_35" : (moltype, " C1 C2 C3 C4 PO4 P3 P5 - GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"SAP2_45" : (moltype, " C1 C2 C3 C4 PO4 - P5 P4 GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"SAP3_345": (moltype, " C1 C2 C3 C4 PO4 P3 P5 P4 GL1 GL2 D1A D2A D3A D4A C5A C1B C2B C3B C4B - - "),
"POPI" : (moltype, " C1 C2 C3 C4 PO4 - - - GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"POP1_3" : (moltype, " C1 C2 C3 C4 PO4 P3 - - GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"POP1_4" : (moltype, " C1 C2 C3 C4 PO4 - - P4 GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"POP1_5" : (moltype, " C1 C2 C3 C4 PO4 - P5 - GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"POP2_34" : (moltype, " C1 C2 C3 C4 PO4 P3 - P4 GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"POP2_35" : (moltype, " C1 C2 C3 C4 PO4 P3 P5 - GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"POP2_45" : (moltype, " C1 C2 C3 C4 PO4 - P5 P4 GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"POP3_345": (moltype, " C1 C2 C3 C4 PO4 P3 P5 P4 GL1 GL2 C1A D2A C3A C4A - C1B C2B C3B C4B - - "),
"INO" : (moltype, " C1 C2 C3 C4 - - - - - - - - - - - - - - - - - "),
"INO1_1" : (moltype, " C1 C2 C3 C4 P1 - - - - - - - - - - - - - - - - "),
"INO2_13" : (moltype, " C1 C2 C3 C4 P1 P3 - - - - - - - - - - - - - - - "),
"INO2_14" : (moltype, " C1 C2 C3 C4 P1 P3 - P4 - - - - - - - - - - - - - "),
"INO2_15" : (moltype, " C1 C2 C3 C4 P1 - P5 - - - - - - - - - - - - - - "),
"INO3_134": (moltype, " C1 C2 C3 C4 P1 P3 - P4 - - - - - - - - - - - - - "),
"INO3_135": (moltype, " C1 C2 C3 C4 P1 P3 P5 - - - - - - - - - - - - - - "),
"INO3_145": (moltype, " C1 C2 C3 C4 P1 - P5 P4 - - - - - - - - - - - - - "),
"INO4_1345": (moltype, " C1 C2 C3 C4 PO4 P3 P5 P4 - - - - - - - - - - - - - ")
})


#Prototopology for IPC yeast lipid: MIP2C2OH, MIPC2OH, IPC2OH - Added by HII 2016.01.13
#
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