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
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- Department of Chemisty - -
- University of Rochester - -
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- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sat Oct 29 2005 - 02:53:00 PDT
