AMBER Archive (2008)

Subject: Re: AMBER: ff99 (PK/IDIVF)

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Dec 12 2008 - 08:05:11 CST

the k value used in the dihedral function is pk, but this is the total for
rotating that bond (in this case 14.5). since there are multiple sets of 4
atoms that contribute, the total is divided by the idivf, the expected
number of 4-atom-sets that will have this applied. each will get in this
case 1/4 of the total (1 over the first number after the x-c-c-x in the .dat
file), or 3.625.
the 2 in red is the periodicity of this dihedral term - see
http://ambermd.org/eqn.txt

On Fri, Dec 12, 2008 at 8:26 AM, saurabh agrawal <imsam100_at_yahoo.co.in>wrote:

> Dear Amber Users,
>
>
> In xleap leaprc.ff99 parameters looks like:
> N Pk/IDIVF Po
> ?-c-c-? 2 3.6250 Pi
>
> While In parm99.dat file torsional angle parameters are as given:
>
> x-c-c-x 4 14.50 180 2
>
> May some one explain the meaning of Pk/IDIVF (red) field in torsional angle
> parameters in the ff99 force field and and the formula to calculate it.
> Also the caption of the fields in the parm99.dat file.
>
> Sincere regards,
>
> Thanking you in advance.
>
> Saurabh
>
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