Closed leeping closed 3 years ago
The topology building works if I explicitly specify the CONECT records in the pdb.
It seems like this might still need some sort of fix in PDBFile, such as the addition of standard bond perception for deprotonated lysine. Maybe this can be marked bug
?
This is happening quite often for me. Eagerly awaiting a solution 😉
@Astrovicis : Which force field(s) are you attempting to use, out of curiosity?
It looks like amber14/protein.ff14SB.xml
supports deprotonated lysine (LYN), but the residues.xml
lacks a definition for this amino acid variant.
@peastman: What do you think about adding these protonation state variants to residues.xml
? The PDB standard says that CONECT
records are "only mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table". Since the definition of HET residues is vague, it could be interpreted as suggesting that standard amino acid variants / protonation states should be considered as not requiring CONECT
residues.
@Astrovicis : As a workaround, you can add CONECT
records to your PDB file.
What name does the residue have in the PDB file? If it has the standard name LYS, the PDB loader should handle it correctly even if one atom is missing. If the force field then has an appropriate template, it should work. On the other hand, if you've given it a nonstandard name, there's no way the PDB loader can know what it's supposed to be.
Since the definition of HET residues is vague, it could be interpreted as suggesting that standard amino acid variants / protonation states should be considered as not requiring CONECT residues.
The definition is pretty clear. The chemical component dictionary defines exactly what atoms are expected to be present in each standard residue. Missing atoms are tolerated, but the addition of any atom not present in the standard residue definition is not allowed.
The definition is pretty clear. The chemical component dictionary defines exactly what atoms are expected to be present in each standard residue. Missing atoms are tolerated, but the addition of any atom not present in the standard residue definition is not allowed.
That's not quite correct. The chemical component dictionary for HIS
, for example, includes atom names for both delta and epsilon protons and the C-terminal carboxylic acid hydrogen, but it does not include a third amino terminal proton needed if HIS were to appear at the N-terminus of a protein. And yet, despite this, we include this third amino-terminal proton in residues.xml
.
OpenMM fails to build the System for some unconventional amino acids.
The PDB in question is here: https://www.dropbox.com/s/j75p39mrplwhe4p/ace-LYN-nme.pdb
The same error occurs for protonated aspartic acid (ASH) and glutamic acid (GLH), as well as deprotonated cysteine (CYM).