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 - 16:41:38 CDT

Hi
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)

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Monday, April 7, 2008 10:02 pm
Subject: Re: AMBER: how to change the force field parameters inside the prmtop file?
To: amber_at_scripps.edu

> On Mon, Apr 07, 2008, Chih-Ying Lin wrote:
> >
> > Why are the value parameters in the prmtop file only half of the
> value of
> > parameters in the frcmod file after I make a new prmtop file with
> a new
> > frcmod file?
>
> Example, please.
>
> (In general, your posts are very hard to answer because there is
> often way to
> little information given. Providing an input file and a precise
> descriptionof what you did is much more helpful than just saying "I
> did a minimization
> and the answer was not what I expected.")
>
> ...dac
>
> p.s. my WAG is that you may(?) be talking about torsion potentials
> thathave a "division factor" of two.
>
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu