Hey,
I was wondering if there are any parameters for these 3
post-translational modifications in the current AMBER force field.
I tired to generate parameters for palmitoyl-cysteine by using the
lipid21 and ff14sb force fields. I gave the lipid chain the residue name
PA and the amino acid the residue name CYS. I followed the amber manual
(
https://ambermd.org/doc12/Amber22.pdf p. 51). When I tired to tleap
the residues it failed unfortunately, because the carbonyl group of the
fatty acid chain is not defined in the residue PA.
The same thing happened to me when I tried to parameterize
myristoyl-cysteine.
At this stage I would consider 2 alternatives. Either parameterize the
entire residue with the lipid tail, or just parameterize cysteine with
the carbonyl function so that I can use at least the lipid21 parameters
for the lipid tail.
For geranylgeranyl-cysteine I would need to parameterize the entire
residue.
Does anybody have less time-consuming ideas to generate these
parameters? Or does anybody happen to have these parameters at hand?
Best
Eddie
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Received on Mon Dec 04 2023 - 20:00:02 PST
