AMBER Archive (2005)

Subject: RE: AMBER: Improper Torsional Parameters

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 02 2005 - 22:06:28 CST

Dear Ilyas,

There should be no need to divide the number by anything. I believe that if
the initial divider is missing then it defaults to 1. In which case the
number you specify is the value of Vn.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Ilyas Yildirim
> Sent: Wednesday, November 02, 2005 10:01
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Improper Torsional Parameters
>
> 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
> ---------------------------------------------------------------
> - 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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