AMBER Archive (2008)

Subject: AMBER: Negative dihedral coefficients in amber99 - Possible?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun Aug 17 2008 - 21:33:16 CDT

Dear all,

I am doing re-parametrization of some of the dihedral angles defined
for the RNA molecules. In the parm99.dat file, I see that the coefficients
of the dihedral terms are all positive. Is there a physical reason why
they are positive? If not, can I define dihedral terms with negative
coefficients? The fitting I am doing gives negative coefficients. As far
as the calculations are concerned, with these choices, the QM and force
field energies come pretty close to each other. In OPLS, there are
negative coefficients defined for dihedrals, but seeing all the dihedral
coefficients in parm99.dat positive makes me wonder if I am missing
something. Any suggestions are greatly appreciated. Thanks in advance.

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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