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
> /
>
>
>
>
>
>
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Received on Fri Oct 15 2010 - 16:00:04 PDT
