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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 24 2010 - 20:30:02 PST
