vermouth-martinize

vermouth-martinize copied to clipboard

Lipidations are finally published and can be added to the library after some curation: https://zenodo.org/records/10213934

fgrunewald

I had a first stab at making a ProcessorPipeline. I've set it up so that it is a proper recursive DiGraph, but with a convenient `.add` method. I've also mashed...

pckroon

Instead of removing these bonds we should replace them with #ifdef flexibles. At the moment proteins that are a little off in backbone positions are nearly impossible to run. https://github.com/marrink-lab/vermouth-martinize/blob/1593bf140277c85193cf22c5e9ac05222fd590c7/vermouth/data/force_fields/martini3001/aminoacids.ff#L1000-L1010

fgrunewald

parse_pragma cannot handle #include in .itps files which are in #include in the top

3

Hoi, It seems like the ITP reader cannot handle nested includes in the included itps in the top file. This is used (a lot) in Go models and in any...

BartBruininks

The sequence length does not match the number of residues

7

I'm trying to create a coarse-grained model for a virus with an atomic model consisting of 60 chains, each having around 500 amino acids. When I use the following command...

DoubleSheep2

This PR implements a file parser of oxDNA configuration files to read in rotational frames for residues. The initial goal is to use the file parser to implement a frame-based...

jan-stevens

System builder for 100 chains - comment line too long for grompp

14

Hi, I am trying to coarse-grain a protein with 100 chains with each chain having 140 residues using martinize2 but I got an error during the grompp minimization step stating...

kesavanekambaram

Some modifications are missing for the non martini3 force-fields especially for protonation states. Additionally naming schemes of neutral amino acids are not consistent.

fgrunewald

Generating ITP file for use with create_goVirt.py

5

Hello, For proteins that don't start numbering at 1, the .itp file generated by -govs-moltype doesn't match the files generated by create_goVirt.py. For example, I have residues 2-718, but they...

yummy-hat

Issue with odd python version leading to this error

7

The command ``` martinize2 -f combine.pdb -x cg-prot.pdb -o topol.top -p backbone -pf 1000 -elastic -el 0.6 -eu 0.8 ``` were run on two independent workstations. However, one with the...

WillPPK