martini_v3.0_sterols_v1.0.itp

; MARTINI 3 Cholesterol Version 1.0 (April 2023)
; by Luís Borges-Araújo; Ana C. Borges-Araújo; Tugba Nur Ozturk; Daniel P. Ramirez-Echemendia,
; Balázs Fábián, Timothy S. Carpenter; Sebastian Thallmair, Jonathan Barnoud; Helgi I. Ingólfsson;
; Gerhard Hummer; D. Peter Tieleman; Siewert J. Marrink; Paulo C. T. Souza; Manuel N. Melo.
;
; Martini 3 topology of Cholesterol.
; New Martini 3 cholesterol model, addressing issues related to its shape, volume,
; hydrophobicity, and temperature divergence resulting from the bonded setup.
; The proposed model mitigates some limitations of its Martini 2predecessor 
; while maintaining or improving overall behavior as much as possible.
;
; Warning(s)/Note(s):
;   Add define=-DFLEXIBLE to select harmonic bonds for minimization purposes.
;
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;
; When using these parameters please read and cite the parameterization article:
;   Borges-Araújo, L. et al. Martini 3 Coarse-Grained Force Field for cholesterol. (2023) doi: https://doi.org/10.1021/acs.jctc.3c00547
;
; Also be sure to check https://github.com/Martini-Force-Field-Initiative/M3-Sterol-Parameters
; for updates to these parameters.
;
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[ moleculetype ]
; molname  nrexcl
  CHOL     1

[ atoms ]
; i type resnr residue atom cgnr charge  mass    
  1  P1  1     CHOL    ROH  1    0.0     0.0
  2 SC4  1     CHOL    R1   2    0.0   159.8
  3 SC3  1     CHOL    R2   3    0.0   157.0
  4 SC3  1     CHOL    R3   4    0.0     0.0
  5 SC3  1     CHOL    R4   5    0.0     0.0 
  6 TC2  1     CHOL    R5   6    0.0     0.0
  7 TC2  1     CHOL    R6   7    0.0     0.0
  8  C2  1     CHOL    C1   8    0.0   115.2
  9  C2  1     CHOL    C2   9    0.0    72.0

[ bonds ]
; i  j  funct  length  force
  8  9  1     0.440   15000
#ifdef FLEXIBLE
 8  3   1  0.75012  100000
 8  2   1  0.78504  100000
 3  2   1  0.34797  100000
#else
[ constraints ]
 8  3   1  0.75012
 8  2   1  0.78504
 3  2   1  0.34797
#endif

[ angles ]
; i  j  k  funct  angle  force
; Cholesterol acyl chain angle
  5  4  9     1    99.0   250    ;R4-R3-C2

[ dihedrals ]
; i  j  k  l funct  angle  force
; Cholesterol acyl chain tortion
  7  5  4  9   2    -70.0   50  ;R6-R4-R3-C2

[ virtual_sites3 ]
 1   8  3  2  4   1.08999   0.35891   0.22947
 4   8  3  2  4  -0.41067   0.83597  -0.05311
 5   8  3  2  4   0.69138  -0.10352   0.17476
 6   8  3  2  4   0.77524   0.22413   0.92700
 7   8  3  2  4   0.06219   0.32398   0.76967
 
[ exclusions ]
; i  j  k  ...
  1  2  3  4  5  6  7  8
  2  3  4  5  6  7  8
  3  4  5  6  7  8
  4  5  6  7  8 
  5  6  7  8 
  6  7  8 
  7  8