Hi Neha,
It seems that the folder ${AMBERHOME}/dat/leap/parm/ is the place to
start. In it you'll find frcmod.ff03, which contains Yong's dihedral
parameters. However, that's only one of at least two files you'd need, and
the only other one that I see in there is frcmod.ff03ua. You'll also need
all_amino03.lib for the charges and atom types, in
${AMBERHOME}/dat/leap/lib/, but the most important file is a leaprc, such
as "leaprc.ff03." That leaprc file is in ${AMBERHOME}/dat/leap/cmd/oldff/,
which indicates that ff03 is no longer in active development, but there's
nothing wrong with using it. If you need to write a frcmod from scratch,
the format of those things can be found at
http://ambermd.org/formats.html#frcmod
My advice would be to get in touch with the writers of ff03*, and get a
hold of some structures that you can take single point energies of (use the
simplest energy minimization file with one step, run sander, and compare
the results to the benchmark values the ff03* guys can hopefully provide).
This will be an important step to verifying that you have the correct
parameters, since it looks like you'll need to piece together the ff mod
yourself.
After you get that, your goal is to make a leaprc.ff03* file in the form of
leaprc.ff03. Critical elements of that file are references to the
appropriate sub-files (all_amino03.lib, frcmod.ff03*) and a proper listing
of the relevant atom types (you can check some of the current protein force
fields, but notice how there is a divergence of atom types--check to make
sure that you know what everything in ff03* is called). Once you've got
frcmod.ff03* and leaprc.ff03* (perhaps call it leaprc.protein.ff03* to
stick with the new conventions), feel free to contribute--we should keep up
with the various mods.
Dave
On Sun, May 22, 2016 at 9:09 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Hi List,
>
> I was reading papers on ff03* and ff03*. These force fields are available
> for download for gromacs package, however I would like to run it in amber.
> I would l like to know which files are required to be modified in amber to
> include a cosine correction to ψ . i.e. *k*ψ (kcal/mol)
>
> and δψ (deg)
>
>
>
> Many thanks,
> Neha
>
> -
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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>
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Received on Sun May 22 2016 - 19:30:02 PDT
