VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Thu May 05 2016 - 16:25:20 CDT

Hi everyone,

Is there a way to find intermolecular salt bridges in VMD? From what I
understand, the plugin only does intramolecular, i.e. looks for donor and
acceptor in the same atom selection. Is it possible to look for donors and
acceptors in different atomselection?

Specifically, I want to find salt bridges between acidic residues and
choline N (from POPC lipid) and between basic residues and phosphate
oxygens (lipid headgroup).

Regards,
Chitrak.