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Add PTMA AA FF to polyply library [10.1021/acs.macromol.3c00141] #276

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Sep 1, 2023
Merged

Add PTMA AA FF to polyply library [10.1021/acs.macromol.3c00141] #276

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6301581
Add PTMA AA FF to polyply library [arXiv:2209.02072]
ricalessandri Oct 5, 2022
b253dfe
Merge branch 'marrink-lab:master' into PTMA-AA-ff
ricalessandri Aug 21, 2023
adc6800
Use standard OPLS atomtype labels for PTMA
ricalessandri Aug 21, 2023
1f03941
Update citation for PTMA.oplsaa.LigParGen.ff
ricalessandri Aug 21, 2023
9e10144
Somehow, PTMA citation was not working; fixed
ricalessandri Aug 21, 2023
2e207a3
Add test for PTMA AA (opls)
ricalessandri Aug 21, 2023
15b9e79
Add PTMA AA opls to LIBRARY.md
ricalessandri Aug 21, 2023
120b1d6
Re-trigger the test
ricalessandri Aug 21, 2023
bbd2d9e
trigger GitHub actions
ricalessandri Aug 21, 2023
006e37e
Add warning if PTMA is not patched with CH3 groups
ricalessandri Aug 23, 2023
fc5b6e7
Add [non-edges] to [warning] of links_PTMA.ff
ricalessandri Sep 1, 2023
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4 changes: 2 additions & 2 deletions LIBRARY.md
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Expand Up @@ -21,8 +21,8 @@
|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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@@ -0,0 +1,45 @@
;
;;;;;; "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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