Carlos,
by linear I mean that the base pairing remains intact, but the helix
unwinds into a stretched out double strand.
One point just raised by Matt is counterions. Since I didn't add any,
could it have this dramatic effect?
Also, I'll check your equilibration-related post.
Thanks
Sasha
Carlos Simmerling wrote:
> what do you mean by "linear base-paired"?
> also I think your equilibration protocol is probably not nearly
> careful enough- I posted some info on this earlier today so check the
> archives or your amber emails.
>
>
> other things you'll
> On Wed, Apr 22, 2009 at 5:55 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>
>> Hi all,
>> I'm trying to simulate a hairpin structure of RNA using an NMR structure as
>> a starting point (1MFY in PDB). However, the RNA unwinds from a helical
>> structure into a linear base-paired one. This happens within several ns of
>> simulation.
>>
>> I'm using Amber9 with rna.ff99. The initial structure is solvated in TIP3P
>> water box, and the input files are given below.
>> If you have any suggestions or experience simulating structured RNA, any
>> help will be very much appreciated.
>>
>> Thanks
>>
>> Sasha
>>
>>
>>
>> -----
>> initial minimization
>> &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 minimisation whole system
>> &cntrl
>> imin = 1,
>> maxcyc = 10000,
>> ncyc = 5000,
>> ntb = 1,
>> ntr = 0,
>> cut = 15
>> /
>>
>> ----
>> equilibration
>> &cntrl
>> imin = 0,
>> irest = 0,
>> ntx = 1,
>> ntb = 1,
>> cut = 15,
>> ntr = 1,
>> ntc = 2,
>> ntf = 2,
>> tempi = 0.0,
>> temp0 = 300.0,
>> ntt = 3,
>> gamma_ln = 1.0,
>> nstlim = 10000, dt = 0.001,
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>> Keep solute fixed with weak restraints
>> 10.0
>> RES 1 31
>> END
>> END
>>
>> ----
>> Production simulation (repeated in sequence of individual runs)
>> &cntrl
>> imin = 0, irest = 1, ntx = 7,
>> ntb = 2, pres0 = 1.0, ntp = 1,
>> taup = 2.0,
>> cut = 15, ntr = 0,
>> ntc = 2, ntf = 2,
>> tempi = 300.0, temp0 = 300.0,
>> ntt = 3, gamma_ln = 1.0,
>> nstlim = 250000, dt = 0.001,
>> ntpr = 500, ntwx = 500, ntwr = 1000
>> /
>>
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>>
>>
>
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Received on Wed May 20 2009 - 12:18:14 PDT
