In our lab, we are working with a peptide that contains dehydroamino acids, such as dehydrovaline. These residues contain a double bond spanning the alpha and beta carbons. What would be the best Amber atom-type for the alpha and beta carbons? I would like to try the best Amber atom-type but it none will work maybe a GAFF atom type would work. I am new to atom typing in Amber.
!Dehydrovaline residue
!
! | HG11 HG12
! | \ /
! HN--N CG1--HG13
! | /
! | /
! CA==CB
! | \
! | \
! O==C CG2--HG23
! | / \
! | HG21 HG22
Thanks for your advice!
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