AMBER: Force Field Question

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Thu, 27 Apr 2006 17:57:58 -0400 (EDT)

Dear All,

I have a question regarding the force field parameters used in AMBER. I
have created 2 new residues, called isoG and isoC. The diff. of these
residues with the w-c G and C is the transposition of the amino and the
carbonyl groups.

For the RESP charges, I have followed the resp protocol. I am having
some questions regarding the rest of the parameters. Here are a
couple of diagrams (part of G and isoG):
-----------------------------------------------------------------
      - GUANOSINE - - isoGUANOSINE -
            H5 H5
            | |
            CK CK
         / \ / \
  C1' - N* NB C1' - N* NB
        \ / \ /
         CB - CB DH CB - CB H
        / \ / / \ /
      NC C - O ---- > NC CA - N2
        \ / \ \ / \
         CA - NA DH C - NA H
         | \ | \
         N2 H O H
       / \ / \
     H H DH DH
-------------------------------------------------------------------
I need to define a couple of missing dihedral parameters for isoG. For
instance, one that needs to be defined is the following:

H -NA-CA-CB

Before, I used the "H -NA-C -CB" dihedral parameters to define this
missing dih. parameters. Namely;

H -NA-CA-CB 1 1.35 180.0 2. [X -C -NA-X]

The reason why I have chosen this is because isoG and G are not that
different, and by analogy, this looked the best way to define it. But
there is another parameter defined in parm99.dat:

X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230

This particular parameter is used to define the "N2-CA-NA-H ",
"N2-CA-NA-C ", "NC-CA-NA-H " and "NC-CA-NA-C ". But from analogy, I dont
think that this will be a good parameter choice to define the missing
dih. parameter of "H -NA-CA-CB". I wonder what other people in this group
think about this. If I dont define anything for "H -NA-CA-CB", the force
field will use "X -CA-NA-X" parameters for this missing dih. parameter.
But is this reasonable? Thanks in advance.

Best,

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------
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Received on Sun Apr 30 2006 - 06:07:08 PDT
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