AMBER Archive (2009)

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

From: Seetin, Matthew (Matthew_Seetin_at_URMC.Rochester.edu)
Date: Wed Apr 22 2009 - 17:22:29 CDT

Did you add counterions?

--Matt

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of Sasha Buzko
Sent: Wed 4/22/2009 5:55 PM
To: AMBER Mailing List
Subject: [AMBER] Problem with RNA hairpin unwinding in explicit water
 
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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