AMBER Archive (2009)

Subject: Re: [AMBER] Fix the local structure as a rigid body

From: Yunjie Zhao (yjzhao.wh_at_gmail.com)
Date: Tue Jun 16 2009 - 08:57:10 CDT

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_at_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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