search

patrickfuchs / buildH

:computer: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.
https://buildh.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
14 stars 7 forks source link

Beta hydrogens in PS #159

Closed ohsOllila closed 2 years ago

ohsOllila commented 2 years ago

When adding united atom simulation data into the NMRlipids databank, we noticed with @larabort that beta hydrogens in POPS headgroups in Berger and Gromos have a type of "CHdoublebond": https://github.com/patrickfuchs/buildH/blob/master/buildh/lipids/Berger_POPS.json https://github.com/patrickfuchs/buildH/blob/master/buildh/lipids/GROMOSCKP_POPS.json

I am not sure, but my feeling is that "CH" and addition of nitrogen atom in the list would be more appropriate. What do you think?

patrickfuchs commented 2 years ago

Thanks for the comment @ohsOllila, I think you're right. We'll correct that as soon as we can.

patrickfuchs commented 2 years ago

I just checked, indeed this carbon should be a CH with the three helpers that include the neighboring nitrogen.