Dear DAC,
Thanks for your response. I have the following part in my frcmod file:
IMPR
CM-CA-N*-CT 1.0 180. 2. [CM-C -N*-CT]
DH-DH-O -C ??? 180. 2. [Dummy Params]
C -CM-CM-HA 1.1 180. 2. [X -X -CM-HA]
N*-NC-CA-N2 1.1 180. 2. [NA-NC-CA-N2]
For the ??? part, I am not sure what to write. I want to use the following
paramater set for that improper term:
X -X -N2-H 1.0 180. 2. JCC,7,(1986),230
This parameter set is defined for generic case and I dont want to make a
mistake while defining the specific case DH-DH-O -C.
For the proper torsional case, the connection is easy. For instance, lets
say we have the following generic term for the proper torsion:
X -C -C -X 4 14.50 180.0 2. Junmei et al, 1999
If I want to define the proper torsion for (let's say) DH-C -C -DH, this
will be,
DH-C -C -DH 1 3.625 180.0 2.
Anyways, is it proper to use the following improper torsional term in my
frcmod?
DH-DH-O -C 1.1 180. 2. [Dummy Params]
(if I want to make use of "X -X -N2-H 1.0 180. 2.)
Or should I divide/multiply 1.1 with something? Thanks again.
Best,
On Wed, 2 Nov 2005, David A. Case wrote:
> On Fri, Oct 28, 2005, Ilyas Yildirim wrote:
> >
> > Does anyone of u know how the improper torsional parameters enter into the
> > potential energy calculation?
>
> The functional form is the same as for "proper torsions". LEaP identifies all
> atoms that are three-coordinate, and looks to see if the parm file has an
> improper defined for that situation. If so, it uses it; if not, it goes on.
>
> > 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.
>
> "specific" torsions are search for first, and used if a match is found. If
> no match is found, then a search is made to see if a "generic" (aka wild-card)
> torsion with match.
>
> >
> > 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.
>
> Note that, even the functional form for proper and improper torsions is the
> same, they form distinct parameter sets. That is, for proper torsions, only
> the proper torsion section in the parm.dat file is searched for a match.
> Likewise, only torsions that are in the improper part of the parm.dat file
> will be searched for matches for improper torsions.
>
> If you are making frcmod files with improper torsions, be sure to apply
> bugfix.53.
>
> ...good luck...dac
>
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>
--
Ilyas Yildirim
---------------------------------------------------------------
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Received on Wed Nov 02 2005 - 18:53:00 PST
