From: Karol Kaszuba (karol.kaszuba_at_moskit.uwm.edu.pl)
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
dihedral
C6
// \
N1 C5--N7\\
| || C8-H8
C2 C4--N9/
/ \\ / \
H2 N3 \
This same rule as above can be used for other missing parameters.
Good luck!
Regards,
Karol
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