Not yet. I'm running it now, though..
Does anything in the input looks incorrect?
Thanks
Sasha
Carlos Simmerling wrote:
> 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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>>
>>
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Received on Fri Oct 15 2010 - 16:30:02 PDT
