I have a system with lipid-linker-peptide. I have the force field parameters for the lipid as well as for the peptide, but not for the linker (which is a molecular fragment prepared in the lab to link the peptide with the lipid). I want to simulate this system with Gromos53a6 ff and I am not sure how to calculate the parital charges (I have rest of the parameters from the ATB server by Prof. Allen Mark, and I hope that they don't change much). Does anyone know how do they parameterize it to get the partial charges? I have read that the parametrization is done by calculating the free energy of solvation, but I want to know more about the method for this calculation.
http://dx.doi.org/10.1021/ci100335w
One thing to note - free energies of solvation are not used to parametrize the molecules; they are used as validation. There is a loose association of QM calculations (DFT to get electron densities for initial charge assignments) but GROMOS parametrization is highly empirical. Functional groups are pretty transferable, though, so piecing something together from building blocks is usually pretty straightforward unless you have some bizarre linkages that are not covered in the force field.
Hi Justin,
Thanks..! I will give this paper a read.
Also I would like to ask you if you have any experience with the ATB server? Have you come across any reliable/unreliable predictions (of partial charges) made by the ATB server?
PS. I don't think there is any complexity in the linker, it's just one Cyclohexane ring and one Malemide (https://en.wikipedia.org/wiki/Maleimide) ring joined together with one -CH2-
Best,
Swapnil
ATB is pretty good but as with any black box, you must have some idea of how to validate it. No automated method is perfect.
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