Hi everyone.
I'm working on getting parameters for a protein system that has some linker
residues in it. These linkers are nothing too strange, they just have some
amine groups. I can get bonded parameters from the prodrg server. I know the
charge groups are unreliable. I'm using the 53A6 parameter set, and I read how
the charges there were derived. They specifically did the iteration
of parameters manually to give the same charges for the same functional groups.
Does this mean I can take charges from the same functional groups in the rtp
files for amino acids and use those charges in my linkers? If it is necessary
to validate, should that be done on the linkers as molecules in their acidic,
unlinked form? Thanks everyone.
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