vermouth-martinize

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Add option to generate log entries from .ff files

10

This PR adds the option to have martinize2 generate log statements based on .ff files. Blocks, Modifications and Links get debug, info, warning, and error sections, in which each line...

pckroon

Comments

3

This PR implements comment reading and annotation for the itp-reader. It also makes apply_rubber_band label the rubber bands. This PR partially addresses #452 and related issues. With Martini3 it is...

fgrunewald

Reading in header information from itp file

3

I realised I buried this within #483, and might be quite ambitious, but it would be useful to read back in header information (eg. the secondary structure determined by DSSP)...

csbrasnett

Sort nodes to group residues

1

Adds a processor to assign consecutive atomids to molecules, sorted by chain and resid. That way residues will be grouped together in the resulting PDB and ITP file(s). @fgrunewald Is...

pckroon

Default force-content for M3 proteins should be at least 700. https://github.com/marrink-lab/vermouth-martinize/blob/29bc3d5d98fbb070e76f4efcc8491d6671ff069b/bin/martinize2#L425

fgrunewald

Problems with HSE, HSP and ASPP when Martinizing from Charmm36 to M3

5

### These problems were encountered in the latest development version of martinize2/vermouth which was downloaded 18/10-2022. **HSE:** HSE is not present in the M3 forcefield (since HSD and HSE are...

MikkelDA

Problems with -nt -cter and -nter when Martinizing from Charmm36 to M3

3

### These problems were encountered in the latest development version of martinize2/vermouth which was downloaded 18/10-2022. I should preface by saying that martinize2 successfully martinizes the terminals if no terminal-relating...

MikkelDA

Automatic Protonation States via PropKa

3

Apparently the popular propka group has a functional python package. We could leverage this to automatically set pronation states in martinize. https://github.com/jensengroup/propka

fgrunewald

#465 fixed #459, but it disabled the ability to combine elastic network criteria. Currently (after #465 gets merged at least) users can select as `-eunit` either `chain`, `molecule`, `all`, or...

pckroon

modifications make edges in blocks

3

It appears modifications make edges in blocks. I think what happens is that the block + modification is merged and edges between the two are taken from the mapping, sort...

fgrunewald