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.scripps.edu>
>Reply-To: amber.scripps.edu
>To: amber.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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Received on Sun Nov 26 2006 - 06:07:19 PST
