AMBER Archive (2005)

Subject: Re: AMBER: TI - frcmod file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jul 13 2005 - 15:42:49 CDT

Hi Oliver,

I am a little bit confused on one thing. Maybe someone can help me with
this. Now, let's say we load the parameter files from parm99.dat first,
and then the frcmod.03 file. First, the torsional parameters for CT-CT-C
-N will be

CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94
CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94

Then, after the second parameter load (frcmod.03), what will be the
torsional parameters of CT-CT-C -N? I thought that the last column
(above, it is -4 and 2) is defining if there are multiple torsional
parameters for a particular torsion angle. So, if we wanted to change
them, we should have used the following format: (at least that's what I
have understood)

CT-CT-C -N 1 XXXXX XXX -4.
CT-CT-C -N 1 XXXXX XXX 2.

But in frcmod.03 file, the torsional parameters for CT-CT-C -N are defined
as following:

CT-CT-C -N 1 0.0560 0.00 -3.
CT-CT-C -N 1 0.0657 180.00 -2.
CT-CT-C -N 1 0.7784 180.00 1.

I am thinking that these extra three torsional parameters for CT-CT-C -N
are going to be added on the CT-CT-C -N parameter list (because their PN
number are different; -4,2,-3,-2,1). If I am wrong, please correct me. If
it overwrites the parameter list, how does it do it? Just deletes the
whole CT-CT-C -N torsional parameter list previously defined, and then
adds the new parameter list?

But for your case, I totally agree with you. The parameter is already
defined in the force field for H0-CT-C -N. You dont have to change it
to zero. But as I wrote above, I am confused on how the new parameter
list are defined in AMBER when they are loaded. Hope someone can
enlighten us with this.

Best,

On Tue, 12 Jul 2005, Oliver Hucke wrote:

> Hi Ilyas,
>
> thanks for your detailed reply!
>
> So far I have one remark:
>
> > I have checked out the ff03 parameters. The parameters for your system are
> > defined in frcmod.ff03 and parm99.dat. Here are the parameters:
> > - parm99.dat -
> > CT-CT-C -N 1 0.100 0.0 -4. phi,psi,parm94
> > CT-CT-C -N 1 0.07 0.0 2. phi,psi,parm94
> > ---------------
> > - frcmod.ff03 -
> > CT-CT-C -N 1 0.0560 0.00 -3.
> > CT-CT-C -N 1 0.0657 180.00 -2.
> > CT-CT-C -N 1 0.7784 180.00 1.
> >
> > H0-CT-C -N 1 0.0110 0.00 -2.
> > H0-CT-C -N 1 1.0607 180.00 1.
> > ---------------
> > First the parm99.dat is loaded and then the frcmod.ff03 is loaded. As far
> > as I see, there are 5 torsional parameter defined for CT-CT-C -N. That
> > means that if you do a perturbation from CT-CT-C -N --> H0-CT-C -N, you
> > need to defined 5 torsional parameter for H0-CT-C -N, too. (If I am wrong,
> > please someone correct me)
>
> My understanding is that loading of the frcmod file with new parameters
> for the CT-CT-C -N torsion will OVERWRITE the existing parameters. So,
> after reading the frcmod file, 3 parameters are associated with this
> torsion...
>
> This is also the reason why I do not understand that leap asks for the
> redifinition of torsion parameters that are already loaded.
>
> Thanks again,
> Oliver
>
> 

-- 
  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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