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
before having to resort to using the GAFF method. I have included the
structure below.
!Dehydrovaline residue
!
! | HG11 HG12
! | \ /
! HN--N CG1--HG13
! | /
! | /
! CA==CB
! | \
! | \
! O==C CG2--HG23
! | / \
! | HG21 HG22
Thanks for your advice!
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Received on Sat Aug 05 2017 - 18:30:02 PDT
