I changed the sequence like this {NALA ALA ALA ALA CALA}. And added minimization cycle 10 times (2000). No success. And when I see original structure from xleap it is very strained structure, otherwise backbone is a line. At least Amber should be able to convert this linear backbone into a helix after EM. Thank you
> Date: Wed, 24 Feb 2010 23:06:40 -0500
> Subject: Re: [AMBER] Simple question on EM
> From: jason.swails.gmail.com
> To: amber.ambermd.org
>
> Hello
>
> 2010/2/24 Shaandar Nyamtulga <nyam100.hotmail.com>:
> >
> >
> > Hi. I am a novice to simulation. I made EM on a small oligopeptide, which I designed it in xleap. I was expecting it turn into alpha helix or at least a helix after EM. But it seemed me there is not significant coordinate change, even though EM process gave me some results. The following is my procedure.
> > in xleap:
> > source leaprc.ff03
> > exam=sequence{ALA ALA ALA ALA ALA}
>
> Be careful with this. ALA is defined as an internal alanine residue.
> The two ends should be termini residues (N-terminus always comes
> first). To do this, change the above line to
>
> exam=sequence{NALA ALA ALA ALA CALA}
>
> > saveAmberParm exam prmtop exam.prmcrd
> >
> > Then
> > sander -i min2.in -o exam.min1.out -c exam.prmcrd -r exam.min1.xyz
> >
> > Content of min2.in
> > #200 step ofminimization
> > &cntrl
> > maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
> > /
> >
> > Then I converted exam.min1.xyz into pdb usin ambpdb.
> > Visually I compared it to original structure. Seems no difference.
> > I gave this kind of sequence into I-Tasser, it gave me back a nice helix structure.
> > Where is my mistake?
>
> All you did here was a minimization... (and a very small number of
> minimization steps at that). Unless exam.prmcrd is a very strained
> initial structure, I would not expect exam.prmcrd and exam.min1.xyz to
> be very different in structure. The minimizer will only find a local
> minimum, anyway (which there will probably be many of in a
> polypeptide).
>
> Good luck!
> Jason
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Wed Feb 24 2010 - 21:30:02 PST
