Thanks, Matt.
The electrostatic argument does make sense. I'll experiment with it
tomorrow and will post the outcome.
Sasha
matthew_seetin.urmc.rochester.edu wrote:
> The lack of ions is almost certainly your problem. The conversion of the
> molecule from a double helix to a ladder-like conformation is due to
> expansion of the molecule from the strong electrostatic repulsion of the
> phosphate groups. You need to add counter ions to neutralize the system (at
> least), and you should consider adding some extra salt (both positive and
> negative ions, how many depends on the size of your box) to bring the system
> up to biological salt concentrations. The ions will help further screen the
> repulsion of the phosphate groups and keep your system in a stable A-form
> conformation.
>
> --Matt
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
> Of Sasha Buzko
> Sent: Wednesday, April 22, 2009 6:35 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problem with RNA hairpin unwinding in explicit water
>
> 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
>>> /
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
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Received on Wed May 20 2009 - 12:18:53 PDT
