AMBER Archive (2009)

Subject: [AMBER] reg.targeted molecular dynamics

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Fri Feb 20 2009 - 23:10:50 CST

Dear Amber ,

I have started doing Targeted Molecular Dynamics
for two structurally different system from the same sequence ,

I did it in vaccum after doing all the priliminary steps
and gave a mask to the backbone atoms
my input file is below
-----------------------------------------------------------------
  &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 = 1000
  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 =0.5 ,
  tgtmdfrc = 1.0,
  tgtfitmask= ":1- 40 @ P,O1P,O2P,O5',C5',C4',O4',C1',C4',C6,C5,C2,O2,C4,C3',C2',O3'",
  tgtrmsmask= ":1- 40 @ P,O1P,O2P,O5',C5',C4',O4',C1',C4,C6,C5,C2,O2,C4,C3',C2',O3'",

 /
------------------------------------------------------------------------------------------------------------------------------------
when I gave this to a duplex structure amd the duplex is no more stable it goes in to a structure of a junction ,
which is my reference structure , but one strand is not perfect ,
I have doubt regarding
a) tgtfitmask , here i have selected all the back bone atoms
If one wants to select 1-10 , and 21-30 how it should be given ?
b) Its given in the manual that the tgtfitmask and tgtrmsmask canbe same or different
i am not clear still regarding this
two options ,
so for my first try i gavae all to be same ?

if one wants to give it to be different , what is the basic thing to do ?

thanks in advance
balaji
UOM

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