AMBER Archive (2006)

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

From: a a (patd_2_at_hotmail.com)
Date: Fri Nov 24 2006 - 20:27:26 CST

Dear Cristian,

Yes, I tried, but it seems only read the last line, and did not restrainst
the 0 to 9 residues for me.

Any other suggestions? please help!!!!

best regards,

Annie

>From: cristian obiol <c.obiol_at_qf.ub.es>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: NTR for implicit solvent? How to defin restrain for two
> disconnectedsequences?
>Date: Fri, 24 Nov 2006 11:24:28 +0100
>
>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 escribi?
> > 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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