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 - 09:46:32 PDT
