vermouth-martinize

vermouth-martinize copied to clipboard

Automatic Repair of missing PDB coordinates

1

Here is a webserver which also has a pypi package that is separately install able. It repairs protein pdbs adding missing atoms etc. https://pypi.org/project/Pras-Server/ Like with the proPka we could...

fgrunewald

add draft for ff-output

2

An initial draft for a ff-file writer. @pckroon some initial feedback would be appreciated. Once the general layout is good, I write tests.

fgrunewald

Processor multiprocessing

4

This is what i came up with for multiprocessing in the base run_system method. It will always fall back to the old method if `nproc` is not set. So far...

mjtadema

-ff martini model is missing

3

Considering standard non-polarizable protein models, martinize2 has as -ff options elnedyn, elnedyn22 and martini22. It is missing -ff martini, which corresponds to the first protein model created by Luca.

paulocts

slow subgraph

7

it appears nx.subgraph is rather slow, which directly affects a bunch of processes in martinize2. Mostly it is used when making the residue graph. Depending on the complexity of the...

fgrunewald

mapping file mayhem

5

When a modification is part of an atomistic base force-field, it needs to have mapping files in ALL other force-fields, which it can map to. If that is not the...

fgrunewald

-nter and -cter flags do not work for multi-chain molecules

3

For proteins that consist of multiple chains which are connected through e.g. a disulfide bond the -nter and -cter flags don't work. They'll only apply to the terminal residues with...

pckroon

Modification HSP in force field None is not a single connected component

1

hey everyone, Please suggest some alternative solutions that could fix this issue. Thanks a lot. `martinize2 -f /mnt/d/desktop/drot1/drot1.pdb -dssp dssp -scfix -o topol.top -x drot1_CG.pdb -ff martini30b32 -nt -maxwarn 9`...

bwbai

problem parsing `MODEL` entry pdb header

11

Martinize fails at some `MODEL` entries in the pdb header. I did not figure out the exact pattern yet, but if the model number consists out of only a single...

palaou

Make martinize2 accessible in python

1

Couldn't martinize2 exist as a python function too? This way it would be possible to call it directly in python. Ex: ```python from vermouth import martinize2 input_file = 'my/path/to/inp.pdb' output_file...

OLaprevote