Hi,
I am trying to model a protein that contains
4-fluoro-phenylalanine. I've generated an entirely new set of
parameters (using the Generalized Atom Force Field) to use in gromacs.
I understand that I need to modify the .rtp file and aminoacid.dat
files in order to obtain a .top file for the pdb structure (pdb2gmx).
However it isn't clear to me whether I should modify the
ff????_bonded.itp or ff????_non_bonded.itp files with my new parameters?
Alternatively, I could simply use the old force field parameters (in
my case ffamber99) and simply change the para H to an F atom. Would I
do this modification for both the .rtp and ffamber_bonded.itp files only?
Any ideas would be helpful.
Thanks,
Vanessa
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