I am using Gromacs with the Amber FF family. I am able to calculate bonded force constants for post-translationally modified amino acids, but I am unsure of how to calculate the non-bonded LJ parameters for a heterogenous system.
I have derived LJ parameters in the past by comparing bulk properties of a homogenous solvent to experimental properties e.g., density, heat capacity, energy of solvation. However, for my current system I do not have these experimental properties.
I am trying to parameterise a glycated lipid. My system contains:
POPC/DPPC/etc.,
Water
Ions
Glycated-lipids
Hi Stephane,
It has definitely given me food for thought. Thanks for you help, I'll see where I can go from here.
I agree with Stéphane! parameterization of bonds and LJ's coefficients could be done by structural and chemical analogy. But you ought to validate your system by experimental data.
A good place to search it out is the Derek Marsh's Handbook, "Handbook of lipid bilayers" there is lots of information about physicochemical proprerties of lipids, with different polar heads, different hydrocarbon chains, etc. It is a very good and complete handbook, whose gave me a lot of knoledge in the subject in my Ph'D work.
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