[gmx-users] Parameters for unnatural amino acid F-Phe

Vanessa Oklejas voklejas at stanford.edu
Mon May 22 20:52:05 CEST 2006


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.


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