On Sat, Apr 26, 2014, Nitin Sharma wrote:
>
> I am trying to refine docked pose simulated annealing. However, after
> the simulated annealing the structure of protein is completely lost. Can
> someone guide me?
>
> I am following protocol:
>
> # Heating 20ps
> &cntrl
> imin = 0,
> irest = 0,
> ntc=1, ntf=1, ntx = 1,
> ntwx=1000, ntpr = 1000, ntwe=1000, ntwr = 10000,
> ntb = 0, cut = 999.0,
> igb = 5, saltcon=0.2,
> nstlim = 40000, dt = 0.0005,
> ig=-1,
> ntt = 3,
> gamma_ln=50.0,
> tempi=0.0,
> temp0=300.0,
> nmropt=1,
> restraintmask= ':1-386',
> restraint_wt=10,
These restraints are only active if you set ntr=1, which you do not do. If you
look in the mdout file you should see that the positional restraints are never
read in. Then you are heating your protein up to 600 degrees, so of course it
will fall apart. Bottom line: add ntr=1 to your cntrl namelist.
> /
> &ewald
> eedmeth=5,
> /
Oooh...this looks wicked. I *think* it is ignored if igb=5, but I'm not sure.
I would definitely suggest getting rid of this.
...hope this helps....dac
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Received on Fri Apr 25 2014 - 12:30:02 PDT
