it looks good but I strongly suggest igb=5 not 1 (and use mbondi2 radii set
in leap).
also look carefully at the sander output where it tells you how many atoms
match the mask to make sure it is what you want.
On Tue, Jun 16, 2009 at 9:57 AM, Yunjie Zhao <yjzhao.wh.gmail.com> wrote:
> Dear Carlos Simmerling,
>
> Thanks very much for your reply. I may know what you mean. The PDB file has
> 28 residues. I want to fix the local structure (12 to 15, and 18 to 20) as
> a
> rigid body. Is my input file correct?
>
> Iput file:
> MD Generalised Born simulation
> &cntrl
> imin = 0, ntb =0,
> ntr=1,
> restraint_wt=10.0,
> restraintmask=’:12-15,18-20’,
> igb = 1, ntpr = 10000, ntwx = 10000,
> ntt = 3,gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0,
> nstlim = 10000000, dt = 0.001,
> cut = 999
> /
>
> Thanks very much!
>
> Best wishes
>
> Yunjie Zhao
>
> 2009/6/16 Carlos Simmerling <carlos.simmerling.gmail.com>
>
> > it's better to apply strong positional restraints (see the ntr option in
> > the
> > manual) unless you really need the coordinates not to change at all. with
> > restraints and a force constant of 10 to 100, the motion will be very
> > small.
> >
> >
> >
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Received on Mon Jul 06 2009 - 09:46:38 PDT
