diff --git a/LIBRARY.md b/LIBRARY.md index a3e4f339..e4fa0327 100644 --- a/LIBRARY.md +++ b/LIBRARY.md @@ -22,6 +22,7 @@ | | | |[martini3](polyply/data/martini3/PSS.martini3.ff) | |Poly(para-phenylene ethynylene)|PPE | |[martini3](polyply/data/martini3/PPE.martini3.ff) | |Poly(TEMPO methacrylate) |PTMA |[oplsaaLigParGen](polyply/data/oplsaaLigParGen/PTMA.oplsaa.LigParGen.ff)]|[martini3](polyply/data/martini3/PTMA.martini3.ff) | +| | | |[ibi_cgm3](polyply/data/ibi_cmg3/PTMA.cgm3.ibi.ff) | | | | |[ibi_gbcg](polyply/data/ibi_gbcg/PTMA.gbno2.ibi.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) | diff --git a/README.md b/README.md index d7533250..7dab01bd 100644 --- a/README.md +++ b/README.md @@ -39,6 +39,7 @@ force-field, molecule parameters and this program. - (Feb 8, 22') **Featured Research Article in Nature Communcations.** Our article on the polyply software suite is now featured on the [Editors' Highlights](https://www.nature.com/collections/hhfigaahch) for Structural biology, biochemistry and biophysics in Nature Communications. The Editors’ Highlights pages aims to showcase the 50 best papers recently published in an area. The development team is beyond happy to receive this honor. - (May 23, 22') **Fighting Cancer with polyply.** Dane et al. used polyply to setup simulations of vesicles and lipid nanodiscs (LNDs) containing PEGylated lipids, which are used as nanocarriers for cancer therapeutics. They find that LNDs are more effective in delivery likely due to their higher flexibility. Check it out in [Nature Materials](https://www.nature.com/articles/s41563-022-01251-z). - (Jan 18, 23') **Towards whole cell simulations with polyply.** In [a perspective on whole-cell simulations](https://www.frontiersin.org/articles/10.3389/fchem.2023.1106495/full) using the Martini force field, Stevens *et al.* utilize polyply to construct the full 0.5 Mio bp chromosome of the Syn3A minimal cell. This impressive task is a good example of the power of the upcoming DNA implementation into polyply and the role of polyply in the Martini Ecosystem. +- (May 11, 23') **Electronic coarse-grained models in polyply.** Curious about simulating non-conjugated radical-containing polymers for all-organic batteries? The models developed [in this work](https://doi.org/10.1021/acs.macromol.3c00141) for PTMA, or poly(TEMPO acrylamide), are avaiable in polyply. There is an all-atom model and different coarse-grained model (Martini 3, iterative Boltzmann inversion), all of which can be flexibly handled by polyply. ## Contributions & Support We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply diff --git a/polyply/data/ibi_cgm3/PTMA.cgm3.ibi.ff b/polyply/data/ibi_cgm3/PTMA.cgm3.ibi.ff new file mode 100644 index 00000000..1b8f9070 --- /dev/null +++ b/polyply/data/ibi_cgm3/PTMA.cgm3.ibi.ff @@ -0,0 +1,68 @@ +[ moleculetype ] +; name nexcl. +PTMA 2 + +[ info ] +Nonbonded interaction potentials (and example run) can be found at: https://doi.org/10.5281/zenodo.8287521 + +[ atoms ] +; id type resnr residu atom cgnr charge mass + 1 VNL 1 PTMA VNL 1 0.0 54 + 2 EST 1 PTMA EST 2 0.0 54 + 3 C1 1 PTMA C1 3 0.0 54 + 4 C2 1 PTMA C2 4 0.0 54 + 5 C2 1 PTMA C3 5 0.0 54 + 6 N4 1 PTMA N4 6 0.0 36 + +[ bonds ] +; i j funct length + 1 2 1 0.262 15000 { "comment": "M3 PMMA model [10.1038/s41467-021-27627-4] shortened"} + 2 3 1 0.253 15000 { "comment": "PMMA-TEMPO connection"} + 3 4 1 0.326 25000 { "comment": "cog (TEMPO)"} + 3 5 1 0.326 25000 { "comment": "cog (TEMPO)"} + 3 6 1 0.310 100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 4 6 1 0.238 100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 5 6 1 0.238 100000 {"ifdef": "FLEXIBLE", "comment": "cog (TEMPO)"} + +[constraints] +; i j funct length + 3 6 1 0.310 {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 4 6 1 0.238 {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"} + 5 6 1 0.238 {"ifndef": "FLEXIBLE", "comment": "cog (TEMPO)"} + +[ angles ] +; i j k funct length force k + 1 2 3 2 132.9 70 { "comment": "PMMA-TEMPO connection"} + 2 3 4 2 129.0 60 { "comment": "PMMA-TEMPO connection"} + 2 3 5 2 121.9 95 { "comment": "PMMA-TEMPO connection"} + +[dihedrals] +; i j k l funct ref.angle force_k + 3 4 5 6 2 140.00 20 { "comment": "cog (TEMPO)"} + 2 4 5 6 2 150.00 80 { "comment": "PMMA-TEMPO connection"} + +[exclusions] + 1 2 3 4 5 6 + 2 3 4 5 6 + 3 4 5 6 + 4 5 6 + 5 6 + +[ link ] +resname "PTMA" +[ bonds ] +VNL +VNL 1 0.315 4000 {"group": "vinyl backbone"} + +[ link ] +resname "PTMA" +[ angles ] +VNL +VNL ++VNL 2 115 35 {"group": "vinyl backbone"} + +[ link ] +resname "PTMA" +[ angles ] +EST VNL +VNL 2 70 20 + +[ citation ] +2023RAlessandri-Macromolecules +polyply diff --git a/polyply/data/ibi_cgm3/citations.bib b/polyply/data/ibi_cgm3/citations.bib new file mode 100644 index 00000000..1ba4a6f0 --- /dev/null +++ b/polyply/data/ibi_cgm3/citations.bib @@ -0,0 +1,22 @@ + +@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} +} + + +@article{polyply, + title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials}, + author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J}, + journal={Nature Communications}, + doi={10.1038/s41467-021-27627-4}, + year={2022}, + volume={13}, + pages={68} +} diff --git a/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/PTMA.itp b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/PTMA.itp new file mode 100644 index 00000000..1e31b986 --- /dev/null +++ b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/PTMA.itp @@ -0,0 +1,316 @@ +; /Users/alessandri/miniconda3/envs/polyplyRA/bin/polyply gen_params -lib ibi_cgm3 -seq PTMA:10 -o PTMA.itp -name PTMA + +; Please cite the following papers: +; Alessandri, R; de Pablo, J J; Macromolecules 2023; 10.1021/acs.macromol.3c00141 +; Grunewald, F; Alessandri, R; Kroon, P C; Monticelli, L; Souza, P C; Marrink, S J; Nature Communications 2022; 10.1038/s41467-021-27627-4 + +[ moleculetype ] +PTMA 2 + +[ atoms ] + 1 VNL 1 PTMA VNL 1 0.0 54.0 + 2 EST 1 PTMA EST 2 0.0 54.0 + 3 C1 1 PTMA C1 3 0.0 54.0 + 4 C2 1 PTMA C2 4 0.0 54.0 + 5 C2 1 PTMA C3 5 0.0 54.0 + 6 N4 1 PTMA N4 6 0.0 36.0 + 7 VNL 2 PTMA VNL 7 0.0 54.0 + 8 EST 2 PTMA EST 8 0.0 54.0 + 9 C1 2 PTMA C1 9 0.0 54.0 +10 C2 2 PTMA C2 10 0.0 54.0 +11 C2 2 PTMA C3 11 0.0 54.0 +12 N4 2 PTMA N4 12 0.0 36.0 +13 VNL 3 PTMA VNL 13 0.0 54.0 +14 EST 3 PTMA EST 14 0.0 54.0 +15 C1 3 PTMA C1 15 0.0 54.0 +16 C2 3 PTMA C2 16 0.0 54.0 +17 C2 3 PTMA C3 17 0.0 54.0 +18 N4 3 PTMA N4 18 0.0 36.0 +19 VNL 4 PTMA VNL 19 0.0 54.0 +20 EST 4 PTMA EST 20 0.0 54.0 +21 C1 4 PTMA C1 21 0.0 54.0 +22 C2 4 PTMA C2 22 0.0 54.0 +23 C2 4 PTMA C3 23 0.0 54.0 +24 N4 4 PTMA N4 24 0.0 36.0 +25 VNL 5 PTMA VNL 25 0.0 54.0 +26 EST 5 PTMA EST 26 0.0 54.0 +27 C1 5 PTMA C1 27 0.0 54.0 +28 C2 5 PTMA C2 28 0.0 54.0 +29 C2 5 PTMA C3 29 0.0 54.0 +30 N4 5 PTMA N4 30 0.0 36.0 +31 VNL 6 PTMA VNL 31 0.0 54.0 +32 EST 6 PTMA EST 32 0.0 54.0 +33 C1 6 PTMA C1 33 0.0 54.0 +34 C2 6 PTMA C2 34 0.0 54.0 +35 C2 6 PTMA C3 35 0.0 54.0 +36 N4 6 PTMA N4 36 0.0 36.0 +37 VNL 7 PTMA VNL 37 0.0 54.0 +38 EST 7 PTMA EST 38 0.0 54.0 +39 C1 7 PTMA C1 39 0.0 54.0 +40 C2 7 PTMA C2 40 0.0 54.0 +41 C2 7 PTMA C3 41 0.0 54.0 +42 N4 7 PTMA N4 42 0.0 36.0 +43 VNL 8 PTMA VNL 43 0.0 54.0 +44 EST 8 PTMA EST 44 0.0 54.0 +45 C1 8 PTMA C1 45 0.0 54.0 +46 C2 8 PTMA C2 46 0.0 54.0 +47 C2 8 PTMA C3 47 0.0 54.0 +48 N4 8 PTMA N4 48 0.0 36.0 +49 VNL 9 PTMA VNL 49 0.0 54.0 +50 EST 9 PTMA EST 50 0.0 54.0 +51 C1 9 PTMA C1 51 0.0 54.0 +52 C2 9 PTMA C2 52 0.0 54.0 +53 C2 9 PTMA C3 53 0.0 54.0 +54 N4 9 PTMA N4 54 0.0 36.0 +55 VNL 10 PTMA VNL 55 0.0 54.0 +56 EST 10 PTMA EST 56 0.0 54.0 +57 C1 10 PTMA C1 57 0.0 54.0 +58 C2 10 PTMA C2 58 0.0 54.0 +59 C2 10 PTMA C3 59 0.0 54.0 +60 N4 10 PTMA N4 60 0.0 36.0 + +[ bonds ] + 1 2 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened + 2 3 1 0.253 15000 ; PMMA-TEMPO connection + 3 4 1 0.326 25000 ; cog (TEMPO) + 3 5 1 0.326 25000 ; cog (TEMPO) + 7 8 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened + 8 9 1 0.253 15000 ; PMMA-TEMPO connection + 9 10 1 0.326 25000 ; cog (TEMPO) + 9 11 1 0.326 25000 ; cog (TEMPO) +13 14 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +14 15 1 0.253 15000 ; PMMA-TEMPO connection +15 16 1 0.326 25000 ; cog (TEMPO) +15 17 1 0.326 25000 ; cog (TEMPO) +19 20 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +20 21 1 0.253 15000 ; PMMA-TEMPO connection +21 22 1 0.326 25000 ; cog (TEMPO) +21 23 1 0.326 25000 ; cog (TEMPO) +25 26 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +26 27 1 0.253 15000 ; PMMA-TEMPO connection +27 28 1 0.326 25000 ; cog (TEMPO) +27 29 1 0.326 25000 ; cog (TEMPO) +31 32 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +32 33 1 0.253 15000 ; PMMA-TEMPO connection +33 34 1 0.326 25000 ; cog (TEMPO) +33 35 1 0.326 25000 ; cog (TEMPO) +37 38 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +38 39 1 0.253 15000 ; PMMA-TEMPO connection +39 40 1 0.326 25000 ; cog (TEMPO) +39 41 1 0.326 25000 ; cog (TEMPO) +43 44 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +44 45 1 0.253 15000 ; PMMA-TEMPO connection +45 46 1 0.326 25000 ; cog (TEMPO) +45 47 1 0.326 25000 ; cog (TEMPO) +49 50 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +50 51 1 0.253 15000 ; PMMA-TEMPO connection +51 52 1 0.326 25000 ; cog (TEMPO) +51 53 1 0.326 25000 ; cog (TEMPO) +55 56 1 0.262 15000 ; M3 PMMA model [10.1038/s41467-021-27627-4] shortened +56 57 1 0.253 15000 ; PMMA-TEMPO connection +57 58 1 0.326 25000 ; cog (TEMPO) +57 59 1 0.326 25000 ; cog (TEMPO) + +; vinyl backbone + 1 7 1 0.315 4000 + 7 13 1 0.315 4000 +13 19 1 0.315 4000 +19 25 1 0.315 4000 +25 31 1 0.315 4000 +31 37 1 0.315 4000 +37 43 1 0.315 4000 +43 49 1 0.315 4000 +49 55 1 0.315 4000 + +#ifdef FLEXIBLE + 3 6 1 0.310 100000 ; cog (TEMPO) + 4 6 1 0.238 100000 ; cog (TEMPO) + 5 6 1 0.238 100000 ; cog (TEMPO) + 9 12 1 0.310 100000 ; cog (TEMPO) +10 12 1 0.238 100000 ; cog (TEMPO) +11 12 1 0.238 100000 ; cog (TEMPO) +15 18 1 0.310 100000 ; cog (TEMPO) +16 18 1 0.238 100000 ; cog (TEMPO) +17 18 1 0.238 100000 ; cog (TEMPO) +21 24 1 0.310 100000 ; cog (TEMPO) +22 24 1 0.238 100000 ; cog (TEMPO) +23 24 1 0.238 100000 ; cog (TEMPO) +27 30 1 0.310 100000 ; cog (TEMPO) +28 30 1 0.238 100000 ; cog (TEMPO) +29 30 1 0.238 100000 ; cog (TEMPO) +33 36 1 0.310 100000 ; cog (TEMPO) +34 36 1 0.238 100000 ; cog (TEMPO) +35 36 1 0.238 100000 ; cog (TEMPO) +39 42 1 0.310 100000 ; cog (TEMPO) +40 42 1 0.238 100000 ; cog (TEMPO) +41 42 1 0.238 100000 ; cog (TEMPO) +45 48 1 0.310 100000 ; cog (TEMPO) +46 48 1 0.238 100000 ; cog (TEMPO) +47 48 1 0.238 100000 ; cog (TEMPO) +51 54 1 0.310 100000 ; cog (TEMPO) +52 54 1 0.238 100000 ; cog (TEMPO) +53 54 1 0.238 100000 ; cog (TEMPO) +57 60 1 0.310 100000 ; cog (TEMPO) +58 60 1 0.238 100000 ; cog (TEMPO) +59 60 1 0.238 100000 ; cog (TEMPO) +#endif + +[ constraints ] +#ifndef FLEXIBLE + 3 6 1 0.310 ; cog (TEMPO) + 4 6 1 0.238 ; cog (TEMPO) + 5 6 1 0.238 ; cog (TEMPO) + 9 12 1 0.310 ; cog (TEMPO) +10 12 1 0.238 ; cog (TEMPO) +11 12 1 0.238 ; cog (TEMPO) +15 18 1 0.310 ; cog (TEMPO) +16 18 1 0.238 ; cog (TEMPO) +17 18 1 0.238 ; cog (TEMPO) +21 24 1 0.310 ; cog (TEMPO) +22 24 1 0.238 ; cog (TEMPO) +23 24 1 0.238 ; cog (TEMPO) +27 30 1 0.310 ; cog (TEMPO) +28 30 1 0.238 ; cog (TEMPO) +29 30 1 0.238 ; cog (TEMPO) +33 36 1 0.310 ; cog (TEMPO) +34 36 1 0.238 ; cog (TEMPO) +35 36 1 0.238 ; cog (TEMPO) +39 42 1 0.310 ; cog (TEMPO) +40 42 1 0.238 ; cog (TEMPO) +41 42 1 0.238 ; cog (TEMPO) +45 48 1 0.310 ; cog (TEMPO) +46 48 1 0.238 ; cog (TEMPO) +47 48 1 0.238 ; cog (TEMPO) +51 54 1 0.310 ; cog (TEMPO) +52 54 1 0.238 ; cog (TEMPO) +53 54 1 0.238 ; cog (TEMPO) +57 60 1 0.310 ; cog (TEMPO) +58 60 1 0.238 ; cog (TEMPO) +59 60 1 0.238 ; cog (TEMPO) +#endif + +[ angles ] + 1 2 3 2 132.9 70 ; PMMA-TEMPO connection + 2 3 4 2 129.0 60 ; PMMA-TEMPO connection + 2 3 5 2 121.9 95 ; PMMA-TEMPO connection + 7 8 9 2 132.9 70 ; PMMA-TEMPO connection + 8 9 10 2 129.0 60 ; PMMA-TEMPO connection + 8 9 11 2 121.9 95 ; PMMA-TEMPO connection +13 14 15 2 132.9 70 ; PMMA-TEMPO connection +14 15 16 2 129.0 60 ; PMMA-TEMPO connection +14 15 17 2 121.9 95 ; PMMA-TEMPO connection +19 20 21 2 132.9 70 ; PMMA-TEMPO connection +20 21 22 2 129.0 60 ; PMMA-TEMPO connection +20 21 23 2 121.9 95 ; PMMA-TEMPO connection +25 26 27 2 132.9 70 ; PMMA-TEMPO connection +26 27 28 2 129.0 60 ; PMMA-TEMPO connection +26 27 29 2 121.9 95 ; PMMA-TEMPO connection +31 32 33 2 132.9 70 ; PMMA-TEMPO connection +32 33 34 2 129.0 60 ; PMMA-TEMPO connection +32 33 35 2 121.9 95 ; PMMA-TEMPO connection +37 38 39 2 132.9 70 ; PMMA-TEMPO connection +38 39 40 2 129.0 60 ; PMMA-TEMPO connection +38 39 41 2 121.9 95 ; PMMA-TEMPO connection +43 44 45 2 132.9 70 ; PMMA-TEMPO connection +44 45 46 2 129.0 60 ; PMMA-TEMPO connection +44 45 47 2 121.9 95 ; PMMA-TEMPO connection +49 50 51 2 132.9 70 ; PMMA-TEMPO connection +50 51 52 2 129.0 60 ; PMMA-TEMPO connection +50 51 53 2 121.9 95 ; PMMA-TEMPO connection +55 56 57 2 132.9 70 ; PMMA-TEMPO connection +56 57 58 2 129.0 60 ; PMMA-TEMPO connection +56 57 59 2 121.9 95 ; PMMA-TEMPO connection + 2 1 7 2 70 20 + 8 7 13 2 70 20 +14 13 19 2 70 20 +20 19 25 2 70 20 +26 25 31 2 70 20 +32 31 37 2 70 20 +38 37 43 2 70 20 +44 43 49 2 70 20 +50 49 55 2 70 20 + +; vinyl backbone + 1 7 13 2 115 35 + 7 13 19 2 115 35 +13 19 25 2 115 35 +19 25 31 2 115 35 +25 31 37 2 115 35 +31 37 43 2 115 35 +37 43 49 2 115 35 +43 49 55 2 115 35 + +[ dihedrals ] + 3 4 5 6 2 140.00 20 ; cog (TEMPO) + 2 4 5 6 2 150.00 80 ; PMMA-TEMPO connection + 9 10 11 12 2 140.00 20 ; cog (TEMPO) + 8 10 11 12 2 150.00 80 ; PMMA-TEMPO connection +15 16 17 18 2 140.00 20 ; cog (TEMPO) +14 16 17 18 2 150.00 80 ; PMMA-TEMPO connection +21 22 23 24 2 140.00 20 ; cog (TEMPO) +20 22 23 24 2 150.00 80 ; PMMA-TEMPO connection +27 28 29 30 2 140.00 20 ; cog (TEMPO) +26 28 29 30 2 150.00 80 ; PMMA-TEMPO connection +33 34 35 36 2 140.00 20 ; cog (TEMPO) +32 34 35 36 2 150.00 80 ; PMMA-TEMPO connection +39 40 41 42 2 140.00 20 ; cog (TEMPO) +38 40 41 42 2 150.00 80 ; PMMA-TEMPO connection +45 46 47 48 2 140.00 20 ; cog (TEMPO) +44 46 47 48 2 150.00 80 ; PMMA-TEMPO connection +51 52 53 54 2 140.00 20 ; cog (TEMPO) +50 52 53 54 2 150.00 80 ; PMMA-TEMPO connection +57 58 59 60 2 140.00 20 ; cog (TEMPO) +56 58 59 60 2 150.00 80 ; PMMA-TEMPO connection + +[ exclusions ] + 1 2 3 4 5 6 + 2 3 4 5 6 + 3 4 5 6 + 4 5 6 + 5 6 + 7 8 9 10 11 12 + 8 9 10 11 12 + 9 10 11 12 +10 11 12 +11 12 +13 14 15 16 17 18 +14 15 16 17 18 +15 16 17 18 +16 17 18 +17 18 +19 20 21 22 23 24 +20 21 22 23 24 +21 22 23 24 +22 23 24 +23 24 +25 26 27 28 29 30 +26 27 28 29 30 +27 28 29 30 +28 29 30 +29 30 +31 32 33 34 35 36 +32 33 34 35 36 +33 34 35 36 +34 35 36 +35 36 +37 38 39 40 41 42 +38 39 40 41 42 +39 40 41 42 +40 41 42 +41 42 +43 44 45 46 47 48 +44 45 46 47 48 +45 46 47 48 +46 47 48 +47 48 +49 50 51 52 53 54 +50 51 52 53 54 +51 52 53 54 +52 53 54 +53 54 +55 56 57 58 59 60 +56 57 58 59 60 +57 58 59 60 +58 59 60 +59 60 + diff --git a/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command new file mode 100644 index 00000000..7cfea0c6 --- /dev/null +++ b/polyply/tests/test_data/library_tests/ibi_cgm3/PTMA/polyply/command @@ -0,0 +1 @@ +polyply gen_params -lib ibi_cgm3 -seq PTMA:10 -o PTMA.itp -name PTMA diff --git a/polyply/tests/test_lib_files.py b/polyply/tests/test_lib_files.py index d85b2aca..3bfda94a 100644 --- a/polyply/tests/test_lib_files.py +++ b/polyply/tests/test_lib_files.py @@ -189,7 +189,8 @@ def _interaction_equal(interaction1, interaction2, inter_type): ['martini3', 'P3HT'], ['martini3', 'PPE'], ['martini3', 'PTMA'], - ['ibi_gbcg','PTMA'], + ['ibi_cgm3', 'PTMA'], + ['ibi_gbcg', 'PTMA'], ['martini2', 'PEO'], ['martini2', 'PS'], ['martini2', 'PEL'],