AMBER Archive (2009)

Subject: [AMBER] doubt-reg_ Targeted molecular dynamics

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Fri Mar 13 2009 - 11:20:41 CDT

        
        
        
        
        
        
        
        

Dear Amber
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
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 !

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