Hello everyone,
I'm working with a peptide-like molecule that is covalently bonded to a
linker. For the peptide-like part I am using a modified version of the ffG53a6
force field files. The linker section contains an alkyl section, an
oligo-ethylene glycol section (...-O-CH2-CH2-O-CH2-CH2...) and two sulfur atoms.
I am having difficulty finding parameters for this linker section that are
compatible with the peptide section. I can parametrize it with ffgmx, but it
is not compatible with the peptide section when they are combined in the same
molecule. Does anyone have any ideas that might be helpful? Thanks a lot.
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