Dear users,
I need to simulate a protein which is covalently bonded to some
covalent inhibitors using GROMACS 5.0.4 and the AMBER99SB-ILDN force field.
Thanks to the user discussion list I successfully used specbond.dat
and suitable modifications in a local copy of the forcefield to make the
relevant bonds between the protein and the inhibitors. However, I have a
specific question about how account for the effect of the new bonds on the
pre-existing parameters.
As an example, let's take an ester bond with a Glutamate side chain. I
added it to specbond.dat. The GLU side chain partial charges and atom types
should change as a result of the covalent bond. Hence, I created the GLX
residue so I can change its partial charges and atom types. But how should
I derive them?
My idea is to make a GAFF/Antechamber/acpype parametrization of the
ligand bound to a glutamate residue.
By doing this, I will be able to get the charges and atomtypes for the
bonded residue and add them to the forcefield as the "post bond" GLX
residue. Additionally, I will have better parameters for describing this
new bond itself.
Is this approach correct? Any suggestions?
Thank you for your attention,
Leandro.
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