Dear All,
I am new to molecular dynamics, had some tutorials and could run
some initial tests successfully in that they finished without errors
(now to analyze if results make sense).
Now my challenge is to make a molecular dynamics of a homohexamer
which binds to a ssDNS and a co-factor, and that looses some of its
binding capacities when a mutation is present. I could build an
(non-hydrogen) homology model for the system, but I am still facing
some problem on conventions for atom names. I could not overcome
everything still, though.
But in this post I would like to discuss about the best force
fields to use in the main problems I should face: a) a protein monomer
in water; b) a protein oligomer in water; c) a protein bound to an
inhibitor (small organic molecule) in water; d) a protein homohexamer
bound to DNA and co-factor in water.
I spent the last days gathering some information through the web
and the gromacs manual. I could learn a lot, but I feel I still miss
some organization of my understanding. It seems to me that specially
for case "d" (the very one of the moment) an amber force field port
(which best, 99SB?) to gromacs should be the preferred one, right?
Anyway, I would like to make the question wider and ask if someone
might point me to an article/links/whatever, for the to mature this
overview, id est, to a compilation of the preferred (or best) force
field for some typical biochemical MD simulations.
Thanks in advance,
Jorge
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