AMBER Archive (2009)

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

From: matthew_seetin_at_urmc.rochester.edu
Date: Wed Apr 22 2009 - 18:59:02 CDT

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_at_ambermd.org [mailto:amber-bounces_at_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_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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