vermouth-martinize
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marrink-lab
Describe and apply transformation on molecular structures and topologies
When the OXT atom in the terminal is missing, martinize recreates that atom. However, the pdb that is given to DSSP contains 'nan' coordinates obviously and DSSP fails. Unfortunately, this...
It may be a nice idea to add a processor at the end of the pipeline that checks for overlaps/clashes. I think the relevant data should come from FF variables...
The PDB distributes an exhaustive list of the molecules contained in the database, including all monomers from biomolecules and all ligands. That list is available at http://www.wwpdb.org/data/ccd in both cif...
If two atoms are two close and cause an extra edge, it can completely break the workflow. Providing all the edges can be inconvenient, or even impossible because of the...
When writing links, you could do e.g. ``` [ link ] resname $dna_resnames [ angles ] BB1 BB2 +BB 2 bb1_bb2_bb {"group": "Backbone linking angles"} [ dihedrals ] BB1 BB2...
If all the atoms underlying a bead are missing, then the coordinates of the bead will be nan. Writing such coordinate should raise a warning. Indeed, the resulting PDB file...
Zero as atom-index is ignored and all interactions are shifted by 1. For example, >[ atoms ] > ;idx atomtype atomname >0 CH2 EC1 >1 OE O1 > 2 CH2...
As it says in the title, neither Link nor Block have a working copy method where you can do: ```python3 link_or_block_copy = link_or_block.copy() assert link_or_block_copy == link_or_block assert link_or_block_copy is...
The RTP parser does not fill the element field, this means that `RepairGraph` has to guess the element from the atomname in a very unspecific manner.
When running Martinize 2 it parses *all* forcefields, instead of just the ones needed. This means that if a FF you don't need and is not yours contains a sytnax...
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Describe and apply transformation on molecular structures and topologies