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 Fri Oct 15 2010 - 15:30:03 PDT
