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Merge pull request #276 from ricalessandri/PTMA-AA-ff
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Add PTMA AA FF to polyply library [10.1021/acs.macromol.3c00141]
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fgrunewald committed Sep 1, 2023
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4 changes: 2 additions & 2 deletions LIBRARY.md
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|Polystyrene sulfonate |PSS | |[martini2](polyply/data/martini2/PSS.martini.2.itp) |
| | | |[martini3](polyply/data/martini3/PSS.martini3.ff) |
|Poly(para-phenylene ethynylene)|PPE | |[martini3](polyply/data/martini3/PPE.martini3.ff) |
|Poly(TEMPO methacrylate) |PTMA | |[martini3](polyply/data/martini3/PTMA.martini3.ff) |
|Poly(TEMPO methacrylate) |PTMA |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)]|[martini3](polyply/data/martini3/PTMA.martini3.ff) |
|Dextran |DEX | |[martini3](polyply/data/martini3/dextran.martini3.ff) |
|DNA nucleobases |Dx, Tx5, Dx3 w/ x=T,G,A,C|[parmbsc1](polyply/data/parmbsc1/dna_final.ff) |[martini2](polyply/data/martini2/DNA_M2.ff) |
|Aminoacids |3 letter code | |[martini3](polyply/data/martini3/aminoacids.ff) |
|Polydimethylsiloxane |PDMS | |[martini3](polyply/data/martini3/PDMS.martini3.ff)
|Polydimethylsiloxane |PDMS | |[martini3](polyply/data/martini3/PDMS.martini3.ff) |
45 changes: 45 additions & 0 deletions polyply/data/oplsaaLigParGen/CH3.ff
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;
;;;;;; "alpha" METHYL TERMINI for PTMA
;
[ moleculetype ]
; Name nrexcl
CH3a 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_135 1 CH3a C1 1 -0.3029 12.0110
2 opls_140 1 CH3a H2 2 0.0694 1.0080
3 opls_140 1 CH3a H3 3 0.0694 1.0080
4 opls_140 1 CH3a H4 4 0.0694 1.0080
[ bonds ]
; ai aj funct c0 c1
2 1 1 0.1090 284512.000
3 1 1 0.1090 284512.000
4 1 1 0.1090 284512.000
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 107.800 276.144
3 1 4 1 107.800 276.144
2 1 4 1 107.800 276.144


;;;;;; "beta" METHYL TERMINI for PTMA
;
[ moleculetype ]
; Name nrexcl
CH3b 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_135 1 CH3b C1 1 -0.1854 12.0110
2 opls_140 1 CH3b H2 2 0.0386 1.0080
3 opls_140 1 CH3b H3 3 0.0386 1.0080
4 opls_140 1 CH3b H4 4 0.0386 1.0080
[ bonds ]
; ai aj funct c0 c1
2 1 1 0.1090 284512.000
3 1 1 0.1090 284512.000
4 1 1 0.1090 284512.000
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 107.800 276.144
3 1 4 1 107.800 276.144
2 1 4 1 107.800 276.144
375 changes: 375 additions & 0 deletions polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff
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12 changes: 12 additions & 0 deletions polyply/data/oplsaaLigParGen/citations.bib
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Expand Up @@ -45,3 +45,15 @@ @article{polyply
volume={13},
pages={68}
}

@article{2023RAlessandri-Macromolecules,
title={Prediction of Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions},
author={Alessandri, Riccardo and de Pablo, Juan J},
journal={Macromolecules},
volume={56},
number={10},
pages={3574-3584},
doi={10.1021/acs.macromol.3c00141},
year={2023}
}

180 changes: 180 additions & 0 deletions polyply/data/oplsaaLigParGen/links_PTMA.ff
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;-------------------------------------
; PTMA-PTMA connection
;-------------------------------------
[link]
resname "PTMA"
[ bonds ]
C17 +C01 1 0.1529 224262.400 {"group": "connection"}
[ angles ]
C01 C17 +C01 1 112.700 488.273 {"group": "connection"}
C17 +C01 +C02 1 112.700 488.273 {"group": "connection"}
C17 +C01 +C03 1 111.100 527.184 {"group": "connection"}
C17 +C01 +C17 1 112.700 488.273 {"group": "connection"}
H38 C17 +C01 1 110.700 313.800 {"group": "connection"}
H39 C17 +C01 1 110.700 313.800 {"group": "connection"}
[ dihedrals ]
+C03 +C01 C17 C01 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"group": "connection"}
+C01 C17 C01 C03 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"group": "connection"}
+C17 +C01 C17 C01 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"group": "connection"}
+C01 C17 C01 C02 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"group": "connection"}
+C02 +C01 C17 C01 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"group": "connection"}
H38 C17 +C01 +C03 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"group": "connection"}
H39 C17 +C01 +C03 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"group": "connection"}
+H38 +C17 +C01 C17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
H38 C17 +C01 +C17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
H39 C17 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
H39 C17 +C01 +C17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
+H39 +C17 +C01 C17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
H38 C17 +C01 +C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
+H18 +C02 +C01 C17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
+H19 +C02 +C01 C17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
+H20 +C02 +C01 C17 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"group": "connection"}
+O04 +C03 +C01 C17 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"group": "connection"}
+O05 +C03 +C01 C17 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"group": "connection"}
[ pairs ]
C02 +C01 1 {"group": "connection"}
C03 +C01 1 {"group": "connection"}
C01 +C02 1 {"group": "connection"}
C01 +C03 1 {"group": "connection"}
C01 +C17 1 {"group": "connection"}
C17 +O04 1 {"group": "connection"}
C17 +O05 1 {"group": "connection"}
+C02 H38 1 {"group": "connection"}
+C03 H38 1 {"group": "connection"}
+C02 H39 1 {"group": "connection"}
+C03 H39 1 {"group": "connection"}
+C17 H38 1 {"group": "connection"}
+C17 H39 1 {"group": "connection"}
C17 +H18 1 {"group": "connection"}
C17 +H19 1 {"group": "connection"}
C17 +H20 1 {"group": "connection"}
C17 +H38 1 {"group": "connection"}
C17 +H39 1 {"group": "connection"}
[link]
; for bonded potentials spanning three residues
resname "PTMA"
[ dihedrals ]
C17 +C01 +C17 ++C01 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"i-j-k", "group":"connection"} ; across three residues
[ pairs ]
C17 ++C01 1 {"comment":"i-j-k", "group":"connection"} ; across three residues



;--------------------------------------------------------------------------
; Termination of PTMA polymer with a CH3 group on the "alpha" carbon
;--------------------------------------------------------------------------
[link]
resname "CH3a|PTMA"
[ atoms ]
C01 {"replace": {"charge": 0.2237}}
[ bonds ]
-C1 C01 1 0.1529 224262.400 {"comment":"alpha-C-link", "group":"termini"}
[ angles ]
-C1 C01 C02 1 112.700 488.273 {"comment":"alpha-C-link", "group":"termini"}
-C1 C01 C03 1 111.100 527.184 {"comment":"alpha-C-link", "group":"termini"}
-C1 C01 C07 1 112.700 488.273 {"comment":"alpha-C-link", "group":"termini"}
C01 -C1 -H2 1 110.700 313.800 {"comment":"alpha-C-link", "group":"termini"}
C01 -C1 -H3 1 110.700 313.800 {"comment":"alpha-C-link", "group":"termini"}
C01 -C1 -H4 1 110.700 313.800 {"comment":"alpha-C-link", "group":"termini"}
[ dihedrals ]
+C01 C07 C01 -C1 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H2 -C1 C01 C03 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H3 -C1 C01 C03 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H4 -C1 C01 C03 3 -0.209 -0.628 0.000 0.837 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H4 -C1 C01 C07 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H4 -C1 C01 C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H2 -C1 C01 C07 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H3 -C1 C01 C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
H20 C02 C01 -C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H2 -C1 C01 C02 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
H18 C02 C01 -C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
H39 C07 C01 -C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
H38 C07 C01 -C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
-H3 -C1 C01 C07 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
H19 C02 C01 -C1 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
O04 C03 C01 -C1 3 0.000 0.000 0.000 -0.000 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
O05 C03 C01 -C1 3 -1.157 -3.471 0.000 4.628 -0.000 0.000 {"comment":"alpha-C-link", "group":"termini"}
[ pairs ]
-C1 O04 1 {"comment":"alpha-C-link", "group":"termini"}
-C1 O05 1 {"comment":"alpha-C-link", "group":"termini"}
-C1 +C01 1 {"comment":"alpha-C-link", "group":"termini"}
-C1 H18 1 {"comment":"alpha-C-link", "group":"termini"}
-C1 H19 1 {"comment":"alpha-C-link", "group":"termini"}
-C1 H20 1 {"comment":"alpha-C-link", "group":"termini"}
-C1 H38 1 {"comment":"alpha-C-link", "group":"termini"}
-C1 H39 1 {"comment":"alpha-C-link", "group":"termini"}
C02 -H2 1 {"comment":"alpha-C-link", "group":"termini"}
C03 -H2 1 {"comment":"alpha-C-link", "group":"termini"}
C07 -H2 1 {"comment":"alpha-C-link", "group":"termini"}
C02 -H3 1 {"comment":"alpha-C-link", "group":"termini"}
C03 -H3 1 {"comment":"alpha-C-link", "group":"termini"}
C07 -H3 1 {"comment":"alpha-C-link", "group":"termini"}
C02 -H4 1 {"comment":"alpha-C-link", "group":"termini"}
C03 -H4 1 {"comment":"alpha-C-link", "group":"termini"}
C07 -H4 1 {"comment":"alpha-C-link", "group":"termini"}



;--------------------------------------------------------------------------
; Termination of PTMA polymer with a CH3 group on the "beta" carbon
;--------------------------------------------------------------------------
[link]
resname "PTMA|CH3b"
[ atoms ]
C17 {"replace": {"charge": 0.1111}}
[ bonds ]
+C1 C17 1 0.1529 224262.400 {"comment":"beta-C-link", "group": "termini"}
[ angles ]
C01 C17 +C1 1 112.700 488.273 {"comment":"beta-C-link", "group": "termini"}
C17 +C1 +H2 1 110.700 313.800 {"comment":"beta-C-link", "group": "termini"}
C17 +C1 +H3 1 110.700 313.800 {"comment":"beta-C-link", "group": "termini"}
C17 +C1 +H4 1 110.700 313.800 {"comment":"beta-C-link", "group": "termini"}
+H2 +C1 +H3 1 107.800 276.144 {"comment":"beta-C-link", "group": "termini"}
+C1 C17 H39 1 110.700 313.800 {"comment":"beta-C-link", "group": "termini"}
+H2 +C1 +H4 1 107.800 276.144 {"comment":"beta-C-link", "group": "termini"}
+C1 C17 H38 1 110.700 313.800 {"comment":"beta-C-link", "group": "termini"}
+H3 +C1 +H4 1 107.800 276.144 {"comment":"beta-C-link", "group": "termini"}
[ dihedrals ]
+C1 C17 C01 C03 3 -4.960 6.286 1.310 -2.636 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+C1 C17 C01 C02 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+C1 C17 C01 -C17 3 2.301 -1.464 0.837 -1.674 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H4 +C1 C17 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H3 +C1 C17 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H2 +C1 C17 C01 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H2 +C1 C17 H39 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H4 +C1 C17 H38 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H2 +C1 C17 H38 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H4 +C1 C17 H39 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H3 +C1 C17 H39 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
+H3 +C1 C17 H38 3 0.628 1.883 0.000 -2.510 -0.000 0.000 {"comment":"beta-C-link", "group": "termini"}
[ pairs ]
-C17 +C1 1 {"comment":"beta-C-link", "group": "termini"}
C02 +C1 1 {"comment":"beta-C-link", "group": "termini"}
C03 +C1 1 {"comment":"beta-C-link", "group": "termini"}
C01 +H2 1 {"comment":"beta-C-link", "group": "termini"}
H38 +H2 1 {"comment":"beta-C-link", "group": "termini"}
H39 +H2 1 {"comment":"beta-C-link", "group": "termini"}
C01 +H3 1 {"comment":"beta-C-link", "group": "termini"}
H38 +H3 1 {"comment":"beta-C-link", "group": "termini"}
H39 +H3 1 {"comment":"beta-C-link", "group": "termini"}
C01 +H4 1 {"comment":"beta-C-link", "group": "termini"}
H38 +H4 1 {"comment":"beta-C-link", "group": "termini"}
H39 +H4 1 {"comment":"beta-C-link", "group": "termini"}

[ link ]
[ atoms ]
C01 {"resname": "PTMA"}
[ warning ]
You should patch PTMA with a CH3a-terminal residue. Use -seq CH3a:1 PTMA:4 CH3b:1
[ non-edges ]
C01 -C1
C01 -C17

[ link ]
[ atoms ]
C17 {"resname": "PTMA"}
[ warning ]
You should patch PTMA with a CH3b-terminal residue. Use -seq CH3a:1 PTMA:4 CH3b:1
[ non-edges ]
C17 +C1
C17 +C01
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