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
