AMBER Archive (2009)

Subject: [AMBER] High RMSD for DNA: A to B transition study

From: BERGY (nucleic81_at_gmail.com)
Date: Fri Mar 06 2009 - 01:26:57 CST

Dear AmberUsers,

I am doing a Simulation of ADNA (12mer) for 10ns using AMBER9. On
analyzing, i find that the RMSD goes well above 20-30 Angstroms. And
visualization I see that 3 of the Bases got flipped out from the
middle of the helix and the helix looks very much straightened like
a ladder.
These are the input that i used for min,heating,equilibration and
production steps.
----------MIN 1---------
ADNA-MIN1 12mer solvent-+ randomized ions
 &cntrl
  imin =1,
  maxcyc = 500,
  ncyc = 500,
  ntb = 1,
  cut = 10,
  ntr = 1
 /
Hold the DNA fixed
500.0
RES 1 24
END
END
-------------MIN2-----------------------------------
ADNA-MIN2 12mer solvent-+ randomized ions
 &cntrl
  imin =1,
  maxcyc = 500,
  ncyc = 350,
  ntb = 1,
  cut = 10,
  ntr = 0
 /
-------------HEATING- 0K -to-300K-----in-10ps--
ADNA-heat 12mer solvent-+ randomized ions
&cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 5000, dt = 0.002,
  ntpr = 100, ntwx = 100, ntwr = 1000
 /
Keep DNA fixed with weak restraints
25.0
RES 1 24
END
END
----------------EQUILIBRATION-----------
-----Note: The restraints was reduced in steps
-----25.0 ->20.0-> 15.0->10.0->5.0-- of 10ps each
------------------------------------------------
ADNA-md1 12mer solvent-+ randomized ions
&cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 10, ntr = 1,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 5000, dt = 0.002,
  ntpr = 100, ntwx = 100, ntwr = 1000
 /
Keep DNA fixed with weak restraints
25.0
RES 1 24
END
END
--------------production---10ns---in 10ps steps
ADNA-md1 12mer solvent-+ randomized ions
&cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 10,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 5000, dt = 0.002,iwrap=1
  ntpr = 100, ntwx = 100, ntwr = 1000
 /
-------------------------------------------------
I am trying variation in this protocol, as given in the papers of
Mackerell group,Cheatham Group. But your insights in what is really
wrong in the protocol could help me modify it.
 Another doubt is,what precaution should one take while trying to use
Protocols specifies for a different Software(say CHARMM) in AMBER9.
Thank you,

regards,
d.k.senthil
Molecukar Biophysics Unit,
Indian Institute of Science,
India.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber