Re: parameterizing a beta aminocyclohexanecarboxylic acid

From: Karol Kaszuba (
Date: Tue Oct 16 2007 - 09:46:31 CDT

Hello Rebeca,

It will be the best to parametrize your molecule based on quantum chemistry
software - GAMESS, GAUSSIAN. However if you do not have an ability
to do it you can use parameters for similar connections specified in the
CHARMM forcefield for example: in your acid you have a dihedral:

        C1-C2-N-H where:
        C1 is the carbon of non-aromatic ring
        C2 is the carbon of non-aromatic ring
        N - is a nitrogen atom to which two hydrogen atoms are bonded
        H - hydrogen atom bonded to your nitrogen
        You will not find (I was checking quickly so I could be wrong) a
        perfect equivalent of this type of dihedral in the CHARMM
        forcefield for proteins, but in the CHARMMM forcefield
        for Carbocyclic (Bicyclo[3.1.0]hexane) sugar analogs
        you will find a similar connection for CSAD (carbocyclic sugar with
        adenine base)
                      H61 H62
                        \ /
                         N6 look at the atoms named as a: C5 C6 N6 H61
                         | -> these COULD be your missing
                       // \
                       N1 C5--N7\\
                       | || C8-H8
                       C2 C4--N9/
                     / \\ / \
               H2 N3 \
        This same rule as above can be used for other missing parameters.
  Good luck!

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