AMBER Archive (2006)

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

From: cristian obiol (c.obiol_at_qf.ub.es)
Date: Fri Nov 24 2006 - 04:24:28 CST

Dear Annie,
You have to change a line in your input :

.
.
.
Keep upper DNA fixed with weak restraints
 10.0
RES 0 9
RES 34 43
END
END

That's all.

Cristian Obiol
Biological Systems Modelling and
Drug Design Research Group
University of Barcelona

El Viernes, 24 de Noviembre de 2006 10:29, a a escribió:
> 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,
> /
>

>
>
> 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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