polyply_1.0

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branched-chain polymer building

3

Thank you for creating such a wonderful toolkit. Using this feature, is it possible to produce a branched-chain polymer with more than three reactive sites within the monomer? 

hirose125

This PR prepares the code to support multiple backmapping protocols with small changes. The main goal is to take out Polyply's default backmapping protocol from the 'Backmap' class and make...

jan-stevens

adding DNA & RNA force-field from: https://fch.upol.cz/ff_ol/gmxOL21.php As validation single point energies were computed and compared to the pdb2gmx obtained ones. To Do: - [x] single point energy calculation as...

fgrunewald

filter molecule for templates

4

This PR sets the stage for some important changes: - instead of matching templates by resnames each residue now requires a template_name attribute. This allows matching of non-identical residues that...

fgrunewald

Raise better error in top-parser

3

**Describe the bug** Turorial brush lipids does not finish. Polyply 1.5.0. ``` polyply gen_coords -p system.top -o struct.gro -res PEO OHter -c bilayer_brush.gro -name test -box 8.0 8.0 33.0 -split...

BartBruininks

Load topology from JSON file

1

Adding support for loading molecule topologies from JSON files. For large and simple systems, JSON-based topology files are easily created and speed up the generation of the topology object tremendously....

jan-stevens

**Describe the bug** The volume of a single bead residue with another VS on top is incorrectly set to zero instead of the bead-size. The cause is the estimate of...

fgrunewald

Contribute PVA OPLS-AA/LigParGen .ff file

1

This is a self-sufficient PVA `ff` file. Usage example to obtain a 10-mer: ``` polyply gen_params -f PVA.ff -name PVA -seq CH3a:1 PVA:10 CH3b:1 -o PVA_n10_oplsLigParGen.itp ``` This is currently...

ricalessandri

**Describe the bug** Currently the topology reader accepts any amount of topology directives. **Expected behavior** It should at least require `defaults` and `atomtypes` to be set otherwise the pre-processing fails....

fgrunewald

fgrunewald