[gmx-users] preferred/best force fields

iulek at interponta.com.br iulek at interponta.com.br
Fri Aug 14 17:35:18 CEST 2009

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,


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