AMBER Archive (2007)

Subject: Re: AMBER: Problem with leaprc

From: yen li (chem_me2000_at_yahoo.com)
Date: Sat Jun 30 2007 - 09:11:47 CDT


Thankyou Dr. Case. 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?
   
  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.

  Regards,
  Yen
  

"David A. Case" <case_at_scripps.edu> wrote:
  On Thu, Jun 28, 2007, yen li wrote:

> I am working with leaprc.ff03. Here i notice while running tleap that two
> parameter files parm99.dat & frcmod.ff03 are loaded. I also notice that
> frcmod.ff03 contains some duplicate torsion parameters e.g. N-CT-C-N (i.e.
> N-CT-C-N parameters occur both in parm99.dat & frcmod.ff03). Does it mean
> that the original parameters are overwritten or they both are used
> together in summation. Also a possible bug, in parm99.dat occurs CT-CT-N
> -C and in frcmod the same occurs as C -N -CT-CT.

The values in the frcmod file over-ride the ones in par99.dat. Be sure you
have applied bugfix.5 (see the Amber web site.)

....dac

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