2010/2/25 Shaandar Nyamtulga <nyam100.hotmail.com>:
>
> 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?
RMS is certainly one way to quantify structural similarity. This can
be done in ptraj or vmd or pymol or any number of other visualization
programs I'm sure.
>
> 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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>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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--
---------------------------------------
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 - 20:00:02 PST
