> I was wondering if someone would have guidance as the correct/best way to
> parameterise (atom type and charges) the linking residue between two
> proteins that are covalently conjugated together through an amide bond
> between the side chain nitrogen of the lysine of one protein to the
> (glycine) C-terminus carboxyl of the other protein ?
0
R1------CN--------R2
H
split this linker/molecule into two elementary building blocks:
0
R1------C-NHMe one capping group added : NME
0
CH3CN--------R2 another capping group added: ACE
H
& set two intra-molecular charge constraints equals zero for the two
added capping groups with the R (i.e. remove from the FF lib) flag.
RED Python has many new features and in particular in your case it
performs (besides charge derivation & FF lib. building) atom typing
for molecular fragments and automatically defines the head/tails of
each fragment when using the mol3 file format:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
