Please, Carlos, I really appreciate that.
Also is there any way to compare 2 PDBs structurally, and calculate similarity in Amber or any other free software?
Thank you
> From: carlos.simmerling.gmail.com
> Date: Thu, 25 Feb 2010 08:12:00 -0500
> Subject: Re: [AMBER] Simple question on EM again
> To: amber.ambermd.org
>
> as an aside, I think the experimental evidence is quite clear that the
> sequence below does NOT form an alpha helix in solution.
> of course, Jason's point remains correct that simple local minimization is
> unlikely to move out of the initial basin. If one wants a helix from leap,
> though, it is straightforward to us the "impose" command to force a helix. I
> think you'll find, though, that with MD it will move to adopt the preferred
> polypro 2 structure ensemble. If you're interested I can provide some
> references for that.
>
>
> 2010/2/25 Shaandar Nyamtulga <nyam100.hotmail.com>
>
> >
> > 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 Thu Feb 25 2010 - 19:30:02 PST
