PLX (1,2-dilauroyl-sn-glycero-3-phosphate) is similar too but no DLPC.
Here's an idea for a possible workflow:
1. When someone adds a new component to an Amber force field, they check if
that component is already included in the PDB chem components dictionary.
2. If it is, they are required to use the PDB's three letter code.
3. If it isn't, they are free to assign any three letter code that is not
already used for some other component in the PDB dictionary (or in Amber's
force fields).
4. Codes for components not yet present in the PDB get added to a
"not_yet_in_pdb.txt" file of some sort that we use for bookkeeping. Every
year, say around release time, someone goes through the codes in this file
and makes sure the components have not yet been added to the PDB. If they
have, code in Amber force fields is changed to the PDB assigned code and
removed from the not_yet_in_pdb list.
Pawel
On Tue, Mar 24, 2015 at 4:03 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > This is good to know - although does anyone know how one goes about
> > getting a residue name 'assigned' in the PDB? I couldn't find DLPC (or
> > it's constituents) in there - although I have to admit to not looking
> > hard.
>
> ...difficult to crystallize lipids...
>
> PLC is in PDB, do not see DLPC. --tom
>
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Received on Wed Mar 25 2015 - 07:30:07 PDT
