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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Received on Wed May 20 2009 - 12:18:06 PDT
