[AMBER] No output_file during SMD with LCOD

From: Ruth Helena Tichauer <rhtichau.laas.fr>
Date: Thu, 17 Nov 2016 11:45:47 +0100

Dear Amber users,

I’ve been trying to run SMD of a protein with its ligand in explicit solvent using as variable type the Linear Combination Of Distances. Although the run has finished with no error messages, the output_file (nat1_smd.txt) is not written. Here is my input file:

NCSU steered MD : LCOD rxn coord
  irest=1, ntx=5,
  ntb=2, pres0=1.0, ntp=1, taup=1.0,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=2.0, ig=-1,
  nstlim=50000, dt=0.001,
  ntpr=25, ntwx=50, ntwr=100, ioutfm=1,
  ntc=2, ntf=2,
  noshakemask = '.2828-2851,2931-2936,5394-5396',
  restraintmask = ':170,185,@CA,C,N',
  qmmask = ':179,186-187,1007',

   output_file = ‘nat1_smd.txt'
   output_freq = 50

      type = LCOD
      i = (5394,5395,2649,5395)
      r = (1.0,-1.0)
      path = (0.9,-0.9)
      harm = (1000.0)
   end variable

end ncsu_smd

To check out, I’ve tried to do the same kind of simulation following the corresponding tutorial (A10) and again, although the run finishes smoothly, with no errors and an effective proton transfer, the output_file (smd.txt) is not written. This is the command I used to launch the calculation using the provided files:

$AMBERHOME/bin/sander -i mdin -p mr.top -c mr_eq.rst -o mr_pd.out -r mr_pd.rst -x mr_pd.nc &

I wonder if I’m missing something from the tutorial.

I’m using Ambertools and Amber 16.

Thank you for any suggestion on this matter,


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Received on Thu Nov 17 2016 - 03:00:02 PST
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