Dear Allan,
> I have a system in which one of the Lysine residues is carboxylated.
> I looked around (ForceField_PTM and ForceField_NCAA) and didn't find where,
> in the forcefield files, this modified residue is parametrized. I did find
> a paper describing its parametrization and utilization inside Amber. (
> https://onlinelibrary.wiley.com/doi/full/10.1002/prot.20596)
>
> Any clue?
the paper you referenced provides most to all necessary information:
On the last page of the supplement document, the authors show a Lewis
structure of carboxylated Lys with atom types used and atomic charges
derived.
With that information, you can directly create a parm99 parameter file
for carboxylated Lys. Whether you'd need any additional parameters for
torsions etc., I cannot tell without looking into the parameter files.
Atomic coordinates for the parameter template may be available from the
QM calculations also provided in the supplement.
Alternatively, you could try to contact the authors and ask for their
original parameter files.
Regards,
Anselm
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Received on Fri Jul 24 2020 - 08:00:05 PDT
