AMBER Archive (2006)

Subject: Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences?

From: a a (patd_2_at_hotmail.com)
Date: Fri Nov 24 2006 - 03:29:26 CST

Dear Prof. Case,

Yes, I try it. But the output list out as follows:

   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
Keep upper DNA fixed with weak restraints

     GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
      Number of atoms in this group = 0
    ----- END OF GROUP READ -----

Is it correct? It is my input file:

Production MD
&cntrl
  imin=0, irest=1, ntx=5, saltcon=0.35
  nstlim=20000, dt=0.002, ntc=1,
  ntpr=100, ntwx=100, ntr=1,
  cut=16, ntb=0, igb=1,
  ntt=3, gamma_ln=1.0,
  tempi=300.0, temp0=300.0,
/
Keep upper DNA fixed with weak restraints
10.0
RES 0 9 34 43
END
END

What is wrong with my input file?

Best regards and please help!

Annie

>From: "David A. Case" <case_at_scripps.edu>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: NTR for implicit solvent? How to defin restrain for
>two disconnected sequences?
>Date: Thu, 23 Nov 2006 23:02:21 -0800
>
>On Fri, Nov 24, 2006, a a wrote:
>
> > I learnt from tutorial 1, section 5 that I can type
> > as follows to define one continuous section to be restrained, but I
>cannot
> > restraint two disconnected sequences. What should I do ?
> >
> > /
> > Keep DNA fixed with weak restraints
> > 10.0
> > RES 1 20
>
>try: RES 1 20 30 60
>
>...dac
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