Dear Sasha,
I am out of lab now, so only shortly.
We never had any ion-associated problems with net-neutralized RNA simulations,
provided starting structures were OK. You can add some NaCl
using the new Tom Cheatham's parameters, for example,
but ions are unlikely cause of your problems.
We were able to simulate stably kink-turn even with no ions,
i.e., with the net-neutral plasma, just the elbow-like fluctuations
were faster.
There obviously are ff problems, any time we identify them
we report them in the papers.
Do you simulate the whole structure or just part of it?
Jiri
> Thank you for the references, Jiri.
> I'll test things with the benchmark case and see how it looks.
>
> In my system, I did add 30 sodium ions to neutralize the backbone
> charges, prior to solvation. In this case, it's roughly equivalent to a
> 5 mM sodium phosphate concentration (the paper mentions 10 mM).
> Do you think I should artificially increase the number of added ions
> (say, to 60), or should I use packmol to explicitly add sodium and
> phosphate ions to match the 10 mM concentration? Would you expect any
> difference from these two approaches? Or should I just add the
> equivalent of 150 mM of Na+ with packmol?
>
> Thanks again
>
> Sasha
>
>
> Jiri Sponer wrote:
> > common net neutralizing should work for RNA, would be around 0.1-0.2 M,
> >
> > If no ions added, then it would be unstable.
> >
> > Jiri
> >
> >
> >
> >> did you include the salt used in the experiment?
> >>
> >> On Fri, Oct 15, 2010 at 6:08 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
> >>
> >>
> >>> Hi all,
> >>> I've been trying to reproduce a structure of a hairpin-folded RNA
> >>> fragment starting from an experimentally determined NMR structure (PDB
> >>> id 1JO7). However, it keeps rapidly unwinding retaining only the base
> >>> pairing, but not the tertiary structure. Typically, it takes only
> >>> several ns to severely unwind. I have tried a variety of input
> >>> parameters, but with little success. The latest input files are given
> >>> below the message.
> >>>
> >>> The last force field I used was ff99bsc0 with counterions added and
> >>> solvated with TIP3P water in a box with 14 A margins. I also tried
> >>> restraining several bases at the cutoff point (where the rest of the
> >>> full RNA would be), but with no positive effect on the conformation of
> >>> the hairpin.
> >>>
> >>> Could you please take a look at the input files in case there is
> >>> something's not right there?
> >>> At this point, there are three possibilities:
> >>> 1. Something is wrong with input, solvation, etc. (i.e. my fault)
> >>> 2. The force field is inadequate for this problem
> >>> 3. The published structure is physiologically irrelevant, and thus
> >>> cannot be reproduced in a stable simulation.
> >>>
> >>>
> >>> I would very much appreciate any advice.
> >>>
> >>> Thanks
> >>>
> >>> Sasha
> >>>
> >>>
> >>>
> >>> Minimization 1
> >>> &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 minimization whole system
> >>> &cntrl
> >>> imin = 1,
> >>> maxcyc = 10000,
> >>> ncyc = 5000,
> >>> ntb = 1,
> >>> ntr = 0,
> >>> cut = 15
> >>> /
> >>>
> >>> Heating
> >>> &cntrl
> >>> imin = 0,
> >>> irest = 0,
> >>> ntx = 1,
> >>> ntb = 1,
> >>> cut = 20,
> >>> ntr = 1,
> >>> ntc = 2,
> >>> ntf = 2,
> >>> tempi = 0.0,
> >>> temp0 = 300.0,
> >>> ntt = 3,
> >>> gamma_ln = 2.0,
> >>> nstlim = 25000, dt = 0.001,
> >>> ntpr = 250, ntwx = 250, ntwr = 1000
> >>> /
> >>> Keep solute fixed with weak restraints
> >>> 10.0
> >>> RES 1 31
> >>> END
> >>> END
> >>>
> >>> Density equilibration
> >>> &cntrl
> >>> imin = 0,
> >>> irest = 1,
> >>> ntx = 5,
> >>> ntb = 2,
> >>> cut = 15,
> >>> ntr = 1,
> >>> ntp = 1,
> >>> ntc = 2,
> >>> ntf = 2,
> >>> temp0 = 300.0,
> >>> ntt = 3,
> >>> gamma_ln = 2.0,
> >>> nstlim = 25000, dt = 0.001,
> >>> ntpr = 250, ntwx = 250, ntwr = 1000
> >>> /
> >>> Keep solute fixed with weak restraints
> >>> 10.0
> >>> RES 1 31
> >>> END
> >>> END
> >>>
> >>>
> >>> First equilibration with some restraints on the solute
> >>> &cntrl
> >>> imin = 0,
> >>> irest = 1,
> >>> ntx = 5,
> >>> ntb = 2,
> >>> cut = 12,
> >>> ntp = 1,
> >>> ntc = 2,
> >>> ntf = 2,
> >>> ntr = 1,
> >>> taup = 2.0,
> >>> temp0 = 300.0,
> >>> ntt = 3,
> >>> tol = 0.000001,
> >>> gamma_ln = 2.0,
> >>> nstlim = 2000000, dt = 0.001,
> >>> ntpr = 10000, ntwx = 10000
> >>> /
> >>> Set
> >>> 10.0
> >>> FIND
> >>> * * B *
> >>> SEARCH
> >>> RES 1 31
> >>> END
> >>> END
> >>>
> >>>
> >>> Full equilibration
> >>> &cntrl
> >>> imin = 0,
> >>> irest = 1,
> >>> ntx = 5,
> >>> ntb = 2,
> >>> cut = 12,
> >>> ntp = 1,
> >>> ntc = 2,
> >>> ntf = 2,
> >>> ntr = 0,
> >>> taup = 2.0,
> >>> temp0 = 300.0,
> >>> ntt = 3,
> >>> tol = 0.000001,
> >>> gamma_ln = 2.0,
> >>> nstlim = 2000000, dt = 0.001,
> >>> ntpr = 10000, ntwx = 10000
> >>> /
> >>>
> >>>
> >>>
> >>> Production simulation (500 ps run - one of many)
> >>> &cntrl
> >>> imin = 0, irest = 1, ntx = 7,
> >>> ntb = 2, pres0 = 1.0, ntp = 1,
> >>> taup = 2.0,
> >>> cut = 10, ntr = 0,
> >>> ntc = 2, ntf = 2,
> >>> temp0 = 300.0,
> >>> ntt = 3, gamma_ln = 2.0,
> >>> nstlim = 250000, dt = 0.002,
> >>> ntpr = 500, ntwx = 500, ntwr = 250000
> >>> /
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
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Received on Sat Oct 16 2010 - 00:30:03 PDT
