AMBER Archive (2008)

Subject: Re: AMBER: how to change the force field parameters inside the prmtop file?

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Tue Apr 08 2008 - 17:39:39 CDT

Hi
How does the phase angle work in the dihedral angle parameter form?

Thanks
Lin

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Tuesday, April 8, 2008 3:11 pm
Subject: Re: AMBER: how to change the force field parameters inside the prmtop file?
To: amber_at_scripps.edu

> On Tue, Apr 08, 2008, Chih-Ying Lin wrote:
> >
> > Here is the example
> >
> > The frcmod file
> > DIHE
> > ca-ne-nf-ca 2 100000 0.000 1.0
> > ca-ca-ne-nf 2 1.43 180 3.0
> > ca-ca-nf-ne 2 1.43 180 3.0
> > ha-ca-ca-ha 2 9.52 0.000 1.0
> > ca-ca-ca-ca 2 9.52 0.000 1.0
> >
> >
> > The prmtop file
> > 52: 0.715 3.14 3.0 :1_at_C5 :1_at_C4 :1_at_N1 :1_at_N2
> (9,11,12,13)> 53: 50000.000 0.00 1.0 :1_at_C4 :1_at_N1
> :1_at_N2 :1_at_C7 (11,12,13,14)
> > 54: 0.715 3.14 3.0 :1_at_N1 :1_at_N2 :1_at_C7 :1_at_C8
> (12,13,14,15)> 55: 0.715 3.14 3.0 :1_at_N1 :1_at_N2
> :1_at_C7 :1_at_C12 (12,13,14,23)
> > 43: 4.760 0.00 1.0 :1_at_C3 :1_at_C2 :1_at_C1 :1_at_C6
> (1,3,5,7)> E 44: 4.760 0.00 1.0 :1_at_C3 :1_at_C4 :1_at_C5
> :1_at_C6 (1,11,9,7)
> >
>
> So: my wild-ass guess (below) was indeed correct:
>
> > > > Why are the value parameters in the prmtop file only half of
> the
> > > value of parameters in the frcmod file
> > >
> > > p.s. my WAG is that you may(?) be talking about torsion
> potentials
> > > that have a "division factor" of two.
> > >
>
> ...dac
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