Dear DAC, Jonathan and Oliver,
Thanks for your answers.
So, if we use the leaprc.ff03 force field, the parameter list for CT-CT-C
-N (for instance) will be
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.
If we are doing a perturbation from CT-CT-C -N to H0-CT-C -N (Oliver's
system), do we have to define 3 different parameter list for H0-CT-C -N in
our frcmod file? The torsional parameters for H0-CT-C -N are defined in
the frcmod.ff03 file as follows:
H0-CT-C -N 1 0.0110 0.00 -2.
H0-CT-C -N 1 1.0607 180.00 1.
If we are going to add an extra 'zero' parameter for H0-CT-C -N (which
leap asks for a 'zero' parameter), I would assume to add the following
lines in my frcmod file, am I wrong?
H0-CT-C -N 1 0.0 0.00 -3.
H0-CT-C -N 1 0.0110 0.00 -2.
H0-CT-C -N 1 1.0607 180.00 1.
Best,
On Wed, 13 Jul 2005, David A. Case wrote:
> On Wed, Jul 13, 2005, Ilyas Yildirim wrote:
> >
> > 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.
>
> Note that only the absolute value of PN matters: 2 is the same as -2.
>
> > 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?
>
> When a frcmod file encounters a set of torsions (like CT-CT-C -N) it indeed
> deletes the whole original set (which may have several Fourier components,
> like 2 and 4 in this exmaple), then adds the new terms (which may also have
> several components, 1,2 and 3 in this example). So you end up with just the
> three components in the frcmod file, and none of the terms that were in the
> original (parm99.dat) file.
>
> In my view, to be fully safe for future code revisions, people who are making
> frcmod files should explicitly override all existing Fourier components. In
> this example, that would mean adding a line like this to frcmod.ff03:
>
> CT-CT-C -N 1 0.0000 0.0 -4.
>
> This would make it uambiguous that the four-fold term in ff03 was not really
> there (==same as being there with a force constant of zero.) This would allow
> simpler algorithms to be used, would guard against bugs (such as in the
> distinct, but similar problem of overriding wild-card torsions with specific
> torsions) and would reduce confusion among humans who look at these files.
>
> ....dac
>
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>
--
Ilyas Yildirim
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Received on Wed Jul 13 2005 - 22:53:00 PDT
