AMBER Archive (2007)

Subject: Re: AMBER: Problem with leaprc

From: yen li (chem_me2000_at_yahoo.com)
Date: Sun Jul 01 2007 - 08:10:09 CDT

Dr. Case, Thankyou for the reply. I am trying to get it out but have found one more thing.
   
  (1) I load leaprc.ff03 in tleap
  (2) I do "desc ff03"
   
  From the output:
  C - N - CT - CT Kp= 0.00 N=4 P0= 180.00 Order: 0123 Desc:
  C - N - CT - CT Kp= 0.06 N=3 P0= 0.00 Order: 0123 Desc:
  C - N - CT - CT Kp= 0.00 N=4 P0= 0.00 Order: 0123 Desc:
  C - N - CT - CT Kp= 0.07 N=2 P0= 180.00 Order: 0123 Desc:
  C - N - CT - CT Kp= 0.78 N=1 P0= 180.00 Order: 0123 Desc:
  C - N - CT - CT Kp= 0.23 N=3 P0= 180.00 Order: 0123 Desc:
  C - N - CT - CT Kp= 0.88 N=2 P0= 180.00 Order: 0123 Desc:
  C - N - CT - CT Kp= 0.35 N=1 P0= 180.00 Order: 0123 Desc:
  
i.e. there are 8 terms for C -N -CT-CT but from the frcmod file, there should be only 4 of them corresponding to:
   
  CT-CT-N -C 1 0.0000 180.0 -4.
C -N -CT-CT 1 0.2270 180.00 -3.
C -N -CT-CT 1 0.8836 180.00 -2.
C -N -CT-CT 1 0.3537 180.00 1.

  -- It so happens that the folloing 4 dihedrals are also treated as C -N -CT-CT. Is it because CT-CT-N-C has -4?
  CT-CT-C -N 1 0.0560 0.00 -3.
CT-CT-C -N 1 0.0000 0.0 -4.
CT-CT-C -N 1 0.0657 180.00 -2.
CT-CT-C -N 1 0.7784 180.00 1.

  Best Regards,
  Yen

"David A. Case" <case_at_scripps.edu> wrote:
  On Sat, Jun 30, 2007, yen li wrote:

> I have downloaded the new parameters tar from AMBER website. In the new
> frcmod.ff03 file, there are two sets for the same dihedral "CT-CT-N -C or C
> -N -CT-CT" that too CT-CT-N -C with force constant 0 (effectively not being
> there at all).
>
> Is there any particular reason for so?

This is to make sure that the non-zero value in parm99.dat for this torsion
is not used.

...dac

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