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}
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?
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Received on Wed Feb 24 2010 - 20:00:03 PST
