AMBER Archive (2009)

Subject: Re: [AMBER] Problem with RNA hairpin unwinding in explicit water

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Apr 22 2009 - 17:53:33 CDT

I don't think leaving out counterions could make it linear (you mean
like a ladder, right?). does it keep the hairpin loop?

this is odd. maybe one of the nucleic acid expert could help. I've
simulated RNA and that has never happened.

On Wed, Apr 22, 2009 at 6:34 PM, Sasha Buzko <obuzko_at_ucla.edu> wrote:
> 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_at_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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