Po is phase, but Pk is NOT omega. it is V. the torsion angle is measured
from the coordinates.
On Sun, Dec 14, 2008 at 1:29 PM, saurabh agrawal <imsam100.yahoo.co.in>wrote:
> Dear Dr. Simmerling and Dr. Walker,
>
> Thank you for your valuable comments and help.
>
> I am just willing to clarify one more query: Is Po stands for phase angle
> (gamma) and Pk/IDIVF is torsion angle (omega)?
>
> Thanking you in advance.
>
> Sincere regards,
>
> Saurabh
>
>
>
> --- On *Fri, 12/12/08, Ross Walker <ross.rosswalker.co.uk>* wrote:
>
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: RE: AMBER: ff99 (PK/IDIVF)
> To: amber.scripps.edu
> Date: Friday, 12 December, 2008, 10:36 PM
>
>
> Hi Saurabh
>
>
>
> To follow up on Carlos's excellent explanation I would just like to add
> that this of course only applies to the use of wildcards (X-) in dihedral
> terms. This is something that has always concerned me in AMBER because it
> makes it very difficult to understand what is going on. Additionally the
> assumption (made by the idivf value) is in my opinion dangerous since one
> could almost certainly find molecules (not necessarily in the amino acid set
> but elsewhere) that had different connectivity for that wild card dihedral.
>
>
>
> My advice if you are generating your own parameters is to ALWAYS explicitly
> define all dihedrals and in all cases set idivf=1 and set the barrier height
> appropriately for that specific dihedral. This will avoid much confusion and
> chances for mistakes.
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Carlos Simmerling
> *Sent:* Friday, December 12, 2008 6:05 AM
> *To:* amber.scripps.edu
> *Subject:* Re: AMBER: ff99 (PK/IDIVF)
>
>
>
> 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.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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Received on Mon Dec 15 2008 - 01:10:16 PST
