AMBER Archive (2008)

Subject: AMBER: equilibration

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Tue Oct 21 2008 - 05:44:54 CDT

Dear amber users,

I am trying to equilibrate the total volume of the water box for 20 ps, at constant pressure (1atm) and
constant temperature (300K), and with positional restraints for CA and the crystal waters.
the input file:
&cntrl
  imin = 0, irest = 0, ntx = 1,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 9, ntr = 1,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 25000, dt = 0.002,
  ntpr = 50, ntwx = 50, ntwr = 50
  restraintmask=':1-300_at_CA&:4799-40288', restraint_wt=10
/
 I am getting such a error:

 Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 68 4641 4639

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

Could somebody help me to track the problem?

Urszula

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