[AMBER] basic question - sanity check

From: Jonathan Gough <jonathan.d.gough.gmail.com>
Date: Wed, 10 Jun 2015 13:48:32 -0400

Hi All,

I want to put restraints on all heavy protein atoms AND the oxygen of a
single water.

I thought I proved this worked in a test case, but from what I can tell, it
didn't work in my production.

I "believe" the line should be:

  ntr=1, restraintmask=':317.O | (!.WAT & !.H)', restraint_wt=25


yes?

The full production input is:

 &cntrl
  imin = 0, nstlim = 10000000, dt = 0.002,
  irest = 1, ntx = 5, ig = -1,
  tempi = 300.0, temp0 = 300.0,
  ntc = 2, ntf = 2, tol = 0.00001,
  tautp = 1.0, taup = 1.0,
  ioutfm = 1
  ntwx = 500, ntwe = 0, ntwr = 500, ntpr = 500,
  cut = 8.0, iwrap = 1,
  ntt =3, gamma_ln = 1.0, ntb = 1, ntp = 0,
  nscm = 0,
  ntr=1, restraintmask=':317.O | (!.WAT & !.H)', restraint_wt=25
 &end


Thanks,
Jonathan
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Received on Wed Jun 10 2015 - 11:00:04 PDT
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