Hi all,
I am trying to convert GROMACS force field parameters to AMBER force field parameters for a protein. I am having a hard time with the RB dihedrals that GROMACS uses. I'm not sure how to convert the coefficients to dihedrals that AMBER can understand. I tried simply converting the coefficients from kj/mol to kc/mol and writing them on separate lines, but that gave me a bit of a weird geometry. I've also tried to work out the math of the Fourier equation, but that gave an odd geometry again. Has anyone done this before and can help me?
Below is an example of the RB dihedrals in GROMACS that I am trying to convert and include in an AMBER frcmod file:
CT CT OS CT 3 2.439272 4.807416 -0.836800 -6.409888 0.000000 0.000000 ;
N CT C N 3 23.84880 7.11280 -16.73600 0.00000 0.00000 0.00000 ; amber99
C N CT C 3 10.46000 -3.34720 -7.11280 0.00000 0.00000 0.00000 ; amber99
CT CT C N 3 0.83680 0.00000 -2.76144 0.00000 3.34720 0.00000 ; amber99
Thank you!
Noureen
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Received on Sat Jan 25 2025 - 01:00:02 PST
