diff --git a/README.md b/README.md index 84e5d6e3..5389774e 100644 --- a/README.md +++ b/README.md @@ -1,47 +1,58 @@ # polyply [![codecov](https://codecov.io/gh/marrink-lab/polyply_1.0/branch/master/graph/badge.svg)](https://codecov.io/gh/marrink-lab/polyply_1.0) +[![Build Status](https://github.com/marrink-lab/polyply_1.0/actions/workflows/python-app.yml/badge.svg)](https://github.com/marrink-lab/polyply_1.0/actions) [![PyPI version](https://badge.fury.io/py/polyply.svg)](https://badge.fury.io/py/polyply) ![license](https://img.shields.io/github/license/marrink-lab/polyply_1.0) ![GitHub Workflow Status](https://img.shields.io/github/workflow/status/marrink-lab/polyply_1.0/Upload%20Python%20Package) [![arXiv](https://img.shields.io/badge/arXiv-2105.05890-b31b1b.svg)](https://arxiv.org/abs/2105.05890) +[![DOI:10.1038/s41467-021-27627-4](https://zenodo.org/badge/DOI/10.1038/s41467-021-27627-4.svg)](https://doi.org/10.1038/s41467-021-27627-4) ## Functionality -Polyply is a python suite designed to facilitate the generation of input files and coordinates for simulating +Polyply is a python suite designed to facilitate the generation of input files and system coordinates for simulating (bio)macromolecules such as synthetic polymers or polysaccharides. Input files can be generated either from user specified building blocks or by using the polymers available in the library. The library currently includes polymer -definitions for the GROMOS and Martini force-fields. The [quick start](https://github.com/marrink-lab/polyply_1.0/wiki/Quick-Start) -section in the wiki gives an overview of the most important commands. In addition some [tutorials][wiki] are provided for more -in-depth information on how to use the program. Tutorials for example include, how to generate -[Martini polymer systems](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts) or +definitions for the GROMOS (2016H66 & 54A6), OPLS, Parmbsc1, and Martini (2 & 3) force-fields. Coordinates are generated +by a multiscale random-walk protocol that is able to generate condensed phase systems at target density, as well as +more heterogeneous systems such as aqueous two phase systems. In addition, polyply allows to tailor initial chain +conformations by providing a build file. For example, the persistence length can be used to control the initial chain +dimensions. The [quick start](https://github.com/marrink-lab/polyply_1.0/wiki/Quick-Start) section in the wiki gives +an overview of the most important commands. In addition, [tutorials][wiki] are provided for more in-depth information +on how to use the program. Tutorials include how to generate +[Martini polymer systems](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts) and [write input files](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-writing-.ff-input-files). -More details on the algorithm and verification can be found in the [publication](https://arxiv.org/abs/2105.05890). +More details on the algorithm and verification can be found in the [publication](https://doi.org/10.1038/s41467-021-27627-4). Make sure to always verify the results and give appropriate credit to the developers of the -force-field, molecule parameters and this program. +force-field, molecule parameters and this program. ## Quick references [Installation Guide](https://github.com/marrink-lab/polyply_1.0/wiki/Installation)\ [FAQs](https://github.com/marrink-lab/polyply_1.0/wiki/FAQs)\ [Submissions to Martini Polymer Library](https://github.com/marrink-lab/polyply_1.0/wiki/Submit-polymer-parameters)\ -[Tutorial Martini Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts)\ -[Tutorial GROMOS Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-GROMOS-polymer-melts) +[Tutorial: Martini Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-martini-polymer-melts)\ +[Tutorial: GROMOS Polymers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-GROMOS-polymer-melts)\ +[Tutorial: PEGylated lipid bilayers](https://github.com/marrink-lab/polyply_1.0/wiki/Tutorial:-PEGylated-lipid-bilayers) -## Contributions -We are happy to accept submissions of polymer parameters (mostly for the Martini force-field). After a small quality control -procedure, parameters are distributed via the Martini library including appropiate citations. To submit parameters simply +## Contributions & Support +We are happy to accept submissions of polymer parameters to the polyply library. To submit parameters simply open an [issue][bug reports]. More details on submitting parameters can be found [here](https://github.com/marrink-lab/polyply_1.0/wiki/Submit-polymer-parameters). The code development of polyply is done -on [github]. Contributions are welcome as [bug reports] and [pull requests] from everyone. +on [github]. Contributions are welcome as [bug reports] and [pull requests] from everyone. We are also happy to discuss +any of your projects or hear about how you used polyply in your research project. Let us know on the +[discussions board](https://github.com/marrink-lab/polyply_1.0/discussions) or by tweeting with #CG_MARTINI or #polyply. ## Citation ``` -@article{grunewald2021polyply, - title={Polyply: a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials}, +@article{Grunewald2022Polyply, + title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials}, author={Gr{\"u}newald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J}, - journal={arXiv preprint arXiv:2105.05890}, - year={2021} + journal={Nature Communications}, + volume={13}, + pages={68}, + doi={https://doi.org/10.1038/s41467-021-27627-4}, + year={2022} } ``` diff --git a/bin/polyply b/bin/polyply index 20ac1e96..c421fb6f 100755 --- a/bin/polyply +++ b/bin/polyply @@ -201,11 +201,11 @@ def main(): # pylint: disable=too-many-locals,too-many-statements "using the connects flag.") seq_group.add_argument('-connects', dest='connects', nargs='+', type=str, help="Provide connect records for sequence. " - "The format is . " + "The format is . " "For example if we want to connect the first and third " "block in a sequence, using a connection between the second " "and third residue in these blocks respectively the input " - "would be <1,3-2,3>.", default=[]) + "would be <1:3:2-3>.", default=[]) seq_group.add_argument('-modf_ter', dest='modifications', nargs='+', type=str, help="change the resname of terminii of a specific block " "in the sequence. The format is .", diff --git a/polyply/data/2016H66/citation.bib b/polyply/data/2016H66/citation.bib new file mode 100644 index 00000000..6728cfaf --- /dev/null +++ b/polyply/data/2016H66/citation.bib @@ -0,0 +1,20 @@ +@article{2016H66, + title={A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set}, + author={Horta, Bruno AC and Merz, Pascal T and Fuchs, Patrick FJ and Dolenc, Jozica and Riniker, Sereina and Hünenberger, Philippe H}, + journal={Journal of chemical theory and computation}, + volume={12}, + number={8}, + pages={3825--3850}, + year={2016}, + publisher={ACS Publications} +} + +@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}, + volume={18}, + pages={382--388}, + doi={10.1038/s41467-021-27627-4}, + year={2022} +} diff --git a/polyply/data/2016H66/polyether_blocks.ff b/polyply/data/2016H66/polyether_blocks.ff index eaa9e0e6..6c9908ce 100644 --- a/polyply/data/2016H66/polyether_blocks.ff +++ b/polyply/data/2016H66/polyether_blocks.ff @@ -1,3 +1,7 @@ +[ citations ] +2016H66 +polyply + [ moleculetype ] PEO 3 [ atoms ] diff --git a/polyply/data/2016H66/polyvinyl_blocks.ff b/polyply/data/2016H66/polyvinyl_blocks.ff index 9c2e9142..93a04798 100644 --- a/polyply/data/2016H66/polyvinyl_blocks.ff +++ b/polyply/data/2016H66/polyvinyl_blocks.ff @@ -1,3 +1,6 @@ +[ citations ] +2016H66 +polyply [ moleculetype ] PE 3 [ atoms ] diff --git a/polyply/data/gromos53A6/P3HT.gromos.53A6.ff b/polyply/data/gromos53A6/P3HT.gromos.53A6.ff index e4fe75f4..f2c4be7f 100755 --- a/polyply/data/gromos53A6/P3HT.gromos.53A6.ff +++ b/polyply/data/gromos53A6/P3HT.gromos.53A6.ff @@ -185,3 +185,4 @@ P3HT 3 [ citations ] P3HT_GROMOS GROMOS53A5and53A6 +polyply diff --git a/polyply/data/gromos53A6/citations.bib b/polyply/data/gromos53A6/citations.bib index a2694e50..9dc406cf 100644 --- a/polyply/data/gromos53A6/citations.bib +++ b/polyply/data/gromos53A6/citations.bib @@ -23,3 +23,14 @@ @article{P3HT_GROMOS doi ={10.1021/jacs.6b11717}, url ={https://doi.org/10.1021/jacs.6b11717} } + + +@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/data/martini2/P3HT.martini.2.itp b/polyply/data/martini2/P3HT.martini.2.itp index 3a237802..b5d82657 100644 --- a/polyply/data/martini2/P3HT.martini.2.itp +++ b/polyply/data/martini2/P3HT.martini.2.itp @@ -66,3 +66,4 @@ P3HT 1 [ citation ] Martini2 P3HT_M2 +polyply diff --git a/polyply/data/martini2/PDADMA.martini.2.itp b/polyply/data/martini2/PDADMA.martini.2.itp index 47c01e25..625aac76 100644 --- a/polyply/data/martini2/PDADMA.martini.2.itp +++ b/polyply/data/martini2/PDADMA.martini.2.itp @@ -39,3 +39,4 @@ PDADMA 2 [ citation ] Martini2 PSS_M2 +polyply diff --git a/polyply/data/martini2/PE.martini.2.itp b/polyply/data/martini2/PE.martini.2.itp index 6e9e12c7..4fea8ed2 100644 --- a/polyply/data/martini2/PE.martini.2.itp +++ b/polyply/data/martini2/PE.martini.2.itp @@ -23,3 +23,4 @@ PE 1 [ citation ] Martini2 PP_PE_M2 +polyply diff --git a/polyply/data/martini2/PEO.martini.2.itp b/polyply/data/martini2/PEO.martini.2.itp index 3c045137..cbe39148 100644 --- a/polyply/data/martini2/PEO.martini.2.itp +++ b/polyply/data/martini2/PEO.martini.2.itp @@ -17,6 +17,7 @@ PEO 1 [ citation ] Martini2 PEO_M2 +polyply [ dihedrals ] 1 2 3 4 1 180.00 1.96 1 1 2 3 4 1 0 0.18 2 diff --git a/polyply/data/martini2/PP.martini.2.itp b/polyply/data/martini2/PP.martini.2.itp index 877f89e1..80f876ce 100644 --- a/polyply/data/martini2/PP.martini.2.itp +++ b/polyply/data/martini2/PP.martini.2.itp @@ -23,3 +23,4 @@ PP 1 [ citation ] Martini2 PP_PE_M2 +polyply diff --git a/polyply/data/martini2/PS.martini.2.itp b/polyply/data/martini2/PS.martini.2.itp index c425ae1e..5a0ef1d5 100644 --- a/polyply/data/martini2/PS.martini.2.itp +++ b/polyply/data/martini2/PS.martini.2.itp @@ -62,3 +62,4 @@ PS 3 [ citation ] Martini2 PS_M2 +polyply diff --git a/polyply/data/martini2/PSS.martini.2.itp b/polyply/data/martini2/PSS.martini.2.itp index f3a347de..3e9ae674 100644 --- a/polyply/data/martini2/PSS.martini.2.itp +++ b/polyply/data/martini2/PSS.martini.2.itp @@ -51,3 +51,4 @@ PSS 3 [ citation ] Martini2 PSS_M2 +polyply diff --git a/polyply/data/martini2/citations.bib b/polyply/data/martini2/citations.bib index 1854ef41..5adad95a 100644 --- a/polyply/data/martini2/citations.bib +++ b/polyply/data/martini2/citations.bib @@ -70,3 +70,12 @@ @article{P3HT_M2 doi={10.1021/jacs.6b11717} } +@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/data/martini2/links.ff b/polyply/data/martini2/links.ff index e41aeea6..d029eef5 100644 --- a/polyply/data/martini2/links.ff +++ b/polyply/data/martini2/links.ff @@ -1,5 +1,6 @@ [ citations ] Martini2 +polyply [ moleculetype ] OHter 1 diff --git a/polyply/data/martini3/P3HT.martini3.ff b/polyply/data/martini3/P3HT.martini3.ff index f70b7464..282deb3b 100644 --- a/polyply/data/martini3/P3HT.martini3.ff +++ b/polyply/data/martini3/P3HT.martini3.ff @@ -1,3 +1,6 @@ +[ citations ] +Martini3 +polyply ; ;;;;; poly(3-hexyl-thiophene) (P3HT) ; [ moleculetype ] diff --git a/polyply/data/martini3/PE.martini3.ff b/polyply/data/martini3/PE.martini3.ff index ac0a86fb..f8a59a3c 100644 --- a/polyply/data/martini3/PE.martini3.ff +++ b/polyply/data/martini3/PE.martini3.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + [ moleculetype ] PE 1 diff --git a/polyply/data/martini3/PEL_link.ff b/polyply/data/martini3/PEL_link.ff index 5d8223fd..90e2af8b 100644 --- a/polyply/data/martini3/PEL_link.ff +++ b/polyply/data/martini3/PEL_link.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + [ link ] resname "DPPE|POPE|DOPE|PEO" [ atoms ] diff --git a/polyply/data/martini3/PEO.martini3.ff b/polyply/data/martini3/PEO.martini3.ff index 59972b13..74b14464 100644 --- a/polyply/data/martini3/PEO.martini3.ff +++ b/polyply/data/martini3/PEO.martini3.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + [ moleculetype ] ; name nexcl. PEO 1 diff --git a/polyply/data/martini3/PMA.martini3.ff b/polyply/data/martini3/PMA.martini3.ff index 72240b5a..3e5c80ee 100644 --- a/polyply/data/martini3/PMA.martini3.ff +++ b/polyply/data/martini3/PMA.martini3.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + [ moleculetype ] PMA 1 ; diff --git a/polyply/data/martini3/PMMA.martini3.ff b/polyply/data/martini3/PMMA.martini3.ff index 759e008a..5f3afb2a 100644 --- a/polyply/data/martini3/PMMA.martini3.ff +++ b/polyply/data/martini3/PMMA.martini3.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + [ moleculetype ] PMMA 1 ; diff --git a/polyply/data/martini3/PS.martini3.ff b/polyply/data/martini3/PS.martini3.ff index 9e7dc678..0c8207c4 100644 --- a/polyply/data/martini3/PS.martini3.ff +++ b/polyply/data/martini3/PS.martini3.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + ; POLYSTYRENE (A-mapping, see ref. below) ; ; diff --git a/polyply/data/martini3/PSS.martini3.ff b/polyply/data/martini3/PSS.martini3.ff index 9594bd79..e320885b 100644 --- a/polyply/data/martini3/PSS.martini3.ff +++ b/polyply/data/martini3/PSS.martini3.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + ; POLYSTYRENE (A-mapping, see ref. below) ; ; diff --git a/polyply/data/martini3/PS_PEO_link.ff b/polyply/data/martini3/PS_PEO_link.ff index ec581f20..6c97533a 100644 --- a/polyply/data/martini3/PS_PEO_link.ff +++ b/polyply/data/martini3/PS_PEO_link.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + [ link ] resname "PS|PEO" [ bonds ] diff --git a/polyply/data/martini3/PVA.martini3.ff b/polyply/data/martini3/PVA.martini3.ff index 2be79dbe..b9a93590 100644 --- a/polyply/data/martini3/PVA.martini3.ff +++ b/polyply/data/martini3/PVA.martini3.ff @@ -1,3 +1,6 @@ +[ citations ] +Martini3 +polyply ; [ moleculetype ] PVA 1 diff --git a/polyply/data/martini3/aminoacids.ff b/polyply/data/martini3/aminoacids.ff index 2bc6260c..747e2699 100644 --- a/polyply/data/martini3/aminoacids.ff +++ b/polyply/data/martini3/aminoacids.ff @@ -22,6 +22,10 @@ stiff_fc 1000000 elastic_network_bond_type 1 res_min_dist 3 +[ citations ] +Martini3 +polyply + ;;; GLYCINE [ moleculetype ] diff --git a/polyply/data/martini3/citations.bib b/polyply/data/martini3/citations.bib new file mode 100644 index 00000000..aaf0e640 --- /dev/null +++ b/polyply/data/martini3/citations.bib @@ -0,0 +1,21 @@ +@article{Martini3, +abstract={The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein–protein and protein–lipid interactions and material science applications as ionic liquids and aedamers.}, +author={Souza, Paulo C T and Alessandri, Riccardo and Barnoud, Jonathan and Thallmair, Sebastian and Faustino, Ignacio and Grünewald, Fabian and Patmanidis, Ilias and Abdizadeh, Haleh and Bruininks, Bart M H and Wassenaar, Tsjerk A and Kroon, Peter C and Melcr, Josef and Nieto, Vincent and Corradi, Valentina and Khan, Hanif M and Domański, Jan and Javanainen, Matti and Martinez-Seara, Hector and Reuter, Nathalie and Best, Robert B and Vattulainen, Ilpo and Monticelli, Luca and Periole, Xavier and Tieleman, D Peter and de Vries, Alex H and Marrink, Siewert J}, +doi={10.1038/s41592-021-01098-3}, +issn={1548-7105}, +journal={Nature Methods}, +title={{Martini 3: a general purpose force field for coarse-grained molecular dynamics}}, +url={https://doi.org/10.1038/s41592-021-01098-3}, +year={2021}, +volume={18}, +pages={382--388} +} +@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/data/martini3/dextran.martini3.ff b/polyply/data/martini3/dextran.martini3.ff index 98fb6b73..2b9ccf46 100644 --- a/polyply/data/martini3/dextran.martini3.ff +++ b/polyply/data/martini3/dextran.martini3.ff @@ -1,3 +1,7 @@ +[ citations ] +Martini3 +polyply + [ moleculetype ] ; molname nrexcl DEX 3 diff --git a/polyply/data/martini3_beta/PEO.martini.3.itp b/polyply/data/martini3_beta/PEO.martini.3.itp index c696b4e0..38bf4aa2 100644 --- a/polyply/data/martini3_beta/PEO.martini.3.itp +++ b/polyply/data/martini3_beta/PEO.martini.3.itp @@ -1,3 +1,6 @@ +[ citations ] +PEO_M2 +polyply [ moleculetype ] ; name nexcl. PEO 1 diff --git a/polyply/data/martini3_beta/citations.bib b/polyply/data/martini3_beta/citations.bib new file mode 100644 index 00000000..0ac8f4b1 --- /dev/null +++ b/polyply/data/martini3_beta/citations.bib @@ -0,0 +1,21 @@ +@article{PEO_M2, + title={Transferable MARTINI model of poly (ethylene oxide)}, + author={Grunewald, Fabian and Rossi, Giulia and de Vries, Alex H and Marrink, Siewert J and Monticelli, Luca}, + journal={The Journal of Physical Chemistry B}, + volume={122}, + number={29}, + pages={7436--7449}, + year={2018}, + publisher={ACS Publications}, + doi={10.1021/acs.jpcb.8b04760} +} + +@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/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff b/polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff index 0b2fdd0c..7112d538 100644 --- a/polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff +++ b/polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff @@ -51,3 +51,4 @@ PEO 3 OPLSLigParGen1 OPLSLigParGen2 OPLSLigParGen3 +polyply diff --git a/polyply/data/oplsaaLigParGen/citations.bib b/polyply/data/oplsaaLigParGen/citations.bib index a01a6b2e..2097cb2a 100644 --- a/polyply/data/oplsaaLigParGen/citations.bib +++ b/polyply/data/oplsaaLigParGen/citations.bib @@ -35,3 +35,13 @@ @article{OPLSLigParGen3 year={2017}, doi={10.1021/acs.jpcb.7b00272} } + +@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/data/parmbsc1/citations.bib b/polyply/data/parmbsc1/citations.bib index 0febbbc6..71c9cbfa 100644 --- a/polyply/data/parmbsc1/citations.bib +++ b/polyply/data/parmbsc1/citations.bib @@ -8,3 +8,13 @@ @article{parmbsc1 year={2016}, publisher={Nature Publishing Group} } + +@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/data/parmbsc1/dna_final.ff b/polyply/data/parmbsc1/dna_final.ff index ce7cf559..1a9f980a 100644 --- a/polyply/data/parmbsc1/dna_final.ff +++ b/polyply/data/parmbsc1/dna_final.ff @@ -3,6 +3,7 @@ base_pairs "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3" [ citations ] parmbsc1 +polyply [ moleculetype ] DA5 3