AMBER Archive (2005)

Subject: AMBER: ATOM TYPE

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon May 16 2005 - 21:10:48 CDT

Dear All,

I have a question on how to define the atom types of a perturbed system.
Let's say that I have a simple molecule, like cytosine. The atom types for
this molecule is described as follows:

                CM - CM H
              / \ /
      R1' - N* CA - N2
              \ / \
                C - NC H
                |
                O

Let's say that we want to transform the -O into -NH2. The question is,
what should be the type of this newly created nitrogen and hydrogen?
Should we use an atom type of 'N2' for the newly created nitrogen and 'H'
type for the hydrogen? Or should we create a new atom type, let's say
'NZ', for the newly created hyrdogen and define all of the parameters for
this atom type (The bond length, angle, dihedrals, nonbonded terms,
etc...)?

As far as I have understood from comparing the nucleic acid structures in
xleap, if an -NH2 is bound to a C, the C type is 'CA' and the N type is
'N2'. And therefore would change the newly created -NH2 with an 'N2' atom
type for N and 'H' atom type for the hydrogen. But I am skeptic about
this, because the position of the newly created -NH2 is close to the sugar
pack. And therefore would expect different parameters for this newly
created atoms. I would like to hear your ideas about this. 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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