AMBER Archive (2007)

Subject: Re: AMBER: Distance restraints between center of mass of two molecules

From: Sudha Mani Karra (karra.md_at_gmail.com)
Date: Wed Aug 15 2007 - 16:02:55 CDT


Carlos,
       Your input was helpful.
I had the following md input file:
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntpr = 100,
  ntwx = 100,
  ntwr = 100,
  ntb = 1,
  ntf = 2,
  ntc = 2,
  cut = 8.0,
  igb = 0,
  nstlim = 10000,
  dt = 0.002,
  ntt = 1,
  ig = 71577,
  tautp = 1.0,
  tempi = 0.0,
  temp0 = 300.0,
  nmropt = 1
 /
&wt
  type = 'END'
/
&rst iat= 1, 6,
     r1= 0.0,
     r2= 9.0,
     r3= 9.0,
     r4= 99.0,
     rk2=1.0,
     rk3=1.0
/

When I look at my .out file, I dont see any restraints that are applied.
--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

ane

 begin time read from input coords = 0.000 ps

           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
                         ** No weight changes given **

 RESTRAINTS:
  No valid redirection requests found
                          ** No restraint defined **

Can you please let me know the error which I made in making my input file?
Also I would like to know how to write these distance deviations (obtained
due to the restraints) into an output file.
Thanks,
Suma

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