AMBER Archive (2005)

Subject: AMBER: Improper Torsional Parameters

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Oct 28 2005 - 19:59:35 CDT

Dear All,

Does anyone of u know how the improper torsional parameters enter into the
potential energy calculation? For instance lets say that we have the
following parameters (extracted from parm99.dat file):

CK-CB-N*-CT 1.0 180. 2.

How are these parameters used in the energy calculation?

In the parm99 file (for example), sometimes the wild-card is used, as it
is done in the following example:

X -X -C -O 10.5 180. 2. JCC,7,(1986),230

The first example is the specific case while the second one is the generic
case. In page # 257 of the AMBER Manual, it is talking about Dihedral
Angle, and how these dihedral parameters are used to calculate the
energies. I am wondering what the difference between generic and specific
case is for improper torsions.

As it is described in the manual, for the dihedrals, if PK=3.0 and
IDIVF=9, then this is used to describe the generic case. As an example,
lets say these parameters are used for the following example. The generic
notation can be as follows:

X -CT-CT-X 9 3.0/2 Phase PN

If we want to use this dihedral definition for a specific case, then the
following can be used:

HC-CT-CT-HC 1 3.0/2/9 Phase PN

For the dihedral case, this is the connection. I could not understand the
connection of the generic and specific cases for the improper torsions.
For example, lets say (again) that we use the following improper torsional
parameter:

X -X -C -O 10.5 180. 2. JCC,7,(1986),230

Can I use the following parameter in my frcmod file (in case I need it)?

NC-CM-C -O 10.5 180. 2.

Or do I have to change something from the original parameter when I skip
into the specific case? 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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