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.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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
---------------------------------
Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 01 2007 - 06:07:51 PDT
