AMBER Archive (2009)

Subject: [AMBER] need- help-for TMD

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Tue Mar 17 2009 - 00:16:34 CDT

Dear Amber !

sorry for posting it for the second time !

I am doing targeted molecular dynamics
for a DNA sequence
 
solved by x ray diffraction , the same
sequence having
 
different structures . One being the
junction and the other being the othe being a
 
duplex the all atom RMSD difference
between the two structures are 14.54 angstroms .
 
 
 
I have already discussed about the
scripts and the tgtfitmask and tgtrmsmask.
 
 
 
I would like to know is it important
that the two structures be energetically equal , that is, they should
 be in the same potential bin or the two
structures can be energetically different and they can be any where
in the potential landscape , and the role of the targeted molecular
dynamics is just taking a target and reference structure moving from
one to the other with an additional term in the energy (restrain).
The structure of the target is moved (TMD is a random walk from one structure to the other )
with the applied force constant (tgtmdfrc) and its co ordinates being
moved at time by doing iterations and converging it towards the
reference coordinates .(does my understanding is right )
 
 
 
 
doubt regarding the flags
 
 
 
 
how to choose a value to the tgtmdfrc
?., ( is it to be done with trial and error)
 
what should be the value given to the
tgtrmsd flag
 
one have to give the maximum rmsd
difference ( 14.54 – in my case ) or it should be the final value
one expect, but in the manual its given that default value is 0 .
 
 
 
I have given my script below , is
there any thing to be included or corrected please let me know !
 
 
 
 
 
 
 
 &cntrl
  imin = 0,
  irest = 0 ,
  ntb = 0,
  ntxo = 1,
  ntx =1,
  tempi =300.0
  ntb = 0,
  ntc=2,
  ntr =0,
  ntf = 2,
  igb = 1,
  nscm = 100,
  ntwr = 100
  ntpr = 100,
  ntwx = 100,
  ntwv =100,
  ntwe = 100,
  ntt = 3,
  gamma_ln = 1.0,
  temp0 = 300.0
  nstlim = 2000000,
  dt = 0.001,
  cut = 12.0,
  itgtmd=1,
  tgtrmsd =0 ,
  tgtmdfrc = 0.1,
  tgtfitmask= ":1- 40"
  tgtrmsmask= ":1- 40"
/
 
 
 
 
 
 
 
 
but when i run this script (its for
vaccum)at initial steps the duplex is moving to wards the junction
very fast and at last the rmsd change is quite stable .
What to be done for this !
 
 
 
 
Could any one suggest a reference paper
regarding TMD using amber
 
 
 
 
thanking you in advance !

balaji
UOM
 
 
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