Dear chun feng,
I am not a user of GROMACS, but I hope someone who's working on
protein dynamics can do me a favor here. I am desperately searching
for a forcefield for free and neutral amino acids. But it seems that
the forcefields such as amber and opls only parametrizes amino
acids in peptides (without OH and H) and terminal amino acids on
peptides.
Yes
I know there has to be some forcefield already developed for popular
molecules like amino acids, anyone please point me the way! Thanks
a million!
You could derive your own force field for such amino-acids. You can
derive RESP and ESP charges for any molecule or molecular fragment
containing chemical elements up to Bromine using the R.E.D. tools. See
http://q4md-forcefieldtools.org/
regards, Francois
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