AMBER Archive (2008)

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

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 08 2008 - 17:08:00 CDT

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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