I would like to try ,make a file by moltemplate.sh and change force field GAFF to MMFF94s.
Is there how to change it?
I’m sorry,short question.
Please thank you.
Dear Murai
I was not aware that any of the popular classII force-fields
(except for DRIEDING) have licenses that allow the force-field
parameters to be shared publicly. Perhaps I'm wrong, however. It
looks like somebody published some software that implements MMFF94 in
RDkit (an open-source program)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116604/
I have a question for you: Do you know where a list of the MMFF94
or MMFF94s force-field parameters can be found? (preferably in an
ordinary text-file)? Presumably, the force-field parameters are
somewhere distributed with the open-source RDkit program:
http://sourceforge.net/projects/rdkit/
If you can find this, then let's talk more.
Keep in mind that I'm not positive that all of the terms in the
force-field are supported by LAMMPS. In particular, I'm not sure
LAMMPS allows you to add an "electrostatic buffering constant" to the
radius when calculating electrostatic interactions:
Ucoul(rij) = qi*qj / ε (rij + δ)
(I found this formula on page 3 of this document:
scc.acad.bg/ncsa/downloads/inst_adapt/MMFF94/Merk Molecular Force
Field.pdf. Perhaps this formula is not used in most MMFF94(s)
force-fields.)
I have very limited time these days, but if we have a complete
list of force-field parameters (in some easy-to-parse file format),
then I can get you started converting those parameters into
moltemplate format.
Keep in mind, this could take some time. Although it did not
take that much time to add OPLSAA support to moltemplate, it did take
a number of months longer for all the various quirks to be reported,
and bug-fixes to be made. In retrospect, I'm not sure I trust
simulations using the OPLSAA which were built using moltemplate, ~6
months after OPLSAA support was officially added.
I hope this gives you an idea. Let me know if you find a list of
MMFF94s force-field parameters, and we can decide what to do from
there.
Cheers
Andrew