common net neutralizing should work for RNA, would be around 0.1-0.2 M,
If no ions added, then it would be unstable.
Jiri
> did you include the salt used in the experiment?
>
> On Fri, Oct 15, 2010 at 6:08 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>
> > Hi all,
> > I've been trying to reproduce a structure of a hairpin-folded RNA
> > fragment starting from an experimentally determined NMR structure (PDB
> > id 1JO7). However, it keeps rapidly unwinding retaining only the base
> > pairing, but not the tertiary structure. Typically, it takes only
> > several ns to severely unwind. I have tried a variety of input
> > parameters, but with little success. The latest input files are given
> > below the message.
> >
> > The last force field I used was ff99bsc0 with counterions added and
> > solvated with TIP3P water in a box with 14 A margins. I also tried
> > restraining several bases at the cutoff point (where the rest of the
> > full RNA would be), but with no positive effect on the conformation of
> > the hairpin.
> >
> > Could you please take a look at the input files in case there is
> > something's not right there?
> > At this point, there are three possibilities:
> > 1. Something is wrong with input, solvation, etc. (i.e. my fault)
> > 2. The force field is inadequate for this problem
> > 3. The published structure is physiologically irrelevant, and thus
> > cannot be reproduced in a stable simulation.
> >
> >
> > I would very much appreciate any advice.
> >
> > Thanks
> >
> > Sasha
> >
> >
> >
> > Minimization 1
> > &cntrl
> > imin = 1,
> > maxcyc = 10000,
> > ncyc = 5000,
> > ntb = 1,
> > ntr = 1,
> > cut = 15
> > /
> > Hold the solute fixed
> > 500.0
> > RES 1 31
> > END
> > END
> >
> > Initial minimization whole system
> > &cntrl
> > imin = 1,
> > maxcyc = 10000,
> > ncyc = 5000,
> > ntb = 1,
> > ntr = 0,
> > cut = 15
> > /
> >
> > Heating
> > &cntrl
> > imin = 0,
> > irest = 0,
> > ntx = 1,
> > ntb = 1,
> > cut = 20,
> > ntr = 1,
> > ntc = 2,
> > ntf = 2,
> > tempi = 0.0,
> > temp0 = 300.0,
> > ntt = 3,
> > gamma_ln = 2.0,
> > nstlim = 25000, dt = 0.001,
> > ntpr = 250, ntwx = 250, ntwr = 1000
> > /
> > Keep solute fixed with weak restraints
> > 10.0
> > RES 1 31
> > END
> > END
> >
> > Density equilibration
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 2,
> > cut = 15,
> > ntr = 1,
> > ntp = 1,
> > ntc = 2,
> > ntf = 2,
> > temp0 = 300.0,
> > ntt = 3,
> > gamma_ln = 2.0,
> > nstlim = 25000, dt = 0.001,
> > ntpr = 250, ntwx = 250, ntwr = 1000
> > /
> > Keep solute fixed with weak restraints
> > 10.0
> > RES 1 31
> > END
> > END
> >
> >
> > First equilibration with some restraints on the solute
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 2,
> > cut = 12,
> > ntp = 1,
> > ntc = 2,
> > ntf = 2,
> > ntr = 1,
> > taup = 2.0,
> > temp0 = 300.0,
> > ntt = 3,
> > tol = 0.000001,
> > gamma_ln = 2.0,
> > nstlim = 2000000, dt = 0.001,
> > ntpr = 10000, ntwx = 10000
> > /
> > Set
> > 10.0
> > FIND
> > * * B *
> > SEARCH
> > RES 1 31
> > END
> > END
> >
> >
> > Full equilibration
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 2,
> > cut = 12,
> > ntp = 1,
> > ntc = 2,
> > ntf = 2,
> > ntr = 0,
> > taup = 2.0,
> > temp0 = 300.0,
> > ntt = 3,
> > tol = 0.000001,
> > gamma_ln = 2.0,
> > nstlim = 2000000, dt = 0.001,
> > ntpr = 10000, ntwx = 10000
> > /
> >
> >
> >
> > Production simulation (500 ps run - one of many)
> > &cntrl
> > imin = 0, irest = 1, ntx = 7,
> > ntb = 2, pres0 = 1.0, ntp = 1,
> > taup = 2.0,
> > cut = 10, ntr = 0,
> > ntc = 2, ntf = 2,
> > temp0 = 300.0,
> > ntt = 3, gamma_ln = 2.0,
> > nstlim = 250000, dt = 0.002,
> > ntpr = 500, ntwx = 500, ntwr = 250000
> > /
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Oct 15 2010 - 16:30:04 PDT
