From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Tue Oct 16 2007 - 12:47:51 CDT
Or perhaps someone on the CHARMM forum at www.charmm.org could help her with this?
They've helped me in the past.
Richard
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal
Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN
55414-2959
rwoodphd_at_yahoo.com
----- Original Message ----
From: Karol Kaszuba <karol.kaszuba_at_moskit.uwm.edu.pl>
To: namd-l_at_ks.uiuc.edu
Sent: Tuesday, October 16, 2007 9:46:31 AM
Subject: Re: namd-l: parameterizing a beta aminocyclohexanecarboxylic acid
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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