Hi!<br>I want to calculate with gromacs, how certain mutations affect the structure of a protein.<br><br>In order to do so, 1st I "mutate" the protein in the pdb file. I use a very simple algorithm, which places the new aa in the same orientation as the old aa was, but it does not ensure that there is no spatial clashes (though in most cases there is no such problem).
<br><br>I run gromacs simulations on this new structure (based on the demo, that comes with it)<br>1st a cg+steep energy minimasition<br>2nd a position restraining<br>3rd a 20ps periodic simulated annealing, with temperatures: 300 320 320 300, and times: 0 2 4 6
<br>4th simple 2ps md at 300K, and I get 10 structures from this run, which then I compare to the wt structure<br><br>What I'm asking is, that is it a reasonable approach? How may I modify it to make it more reasonable?<br>
How may I detect if the protein is in it's favourable conformation? (Mutations in the core may have extensive effects, which may need more time to "settle")<br><br>Any suggestions would be appreciated!<br><br>Hota
<br>