AMBER: SHAKE poblem with dummy atoms

From: Itziar Maestre Asenjo <itziar.qorws1.uab.es>
Date: Tue, 09 Sep 2003 12:06:57 +0200

Dear Amber users

I would like to perform a FEP calculation to study the difference in
energy between a receptor and the two enantiomers of a N-acetyl-alanine.

I have to make the perturbation between a H and a CH3 group, so I have
to add 3 dummies atoms on the H.

I have already build the topology file with the 3 dummies (using leap),
and I have also minimzed the structure.
Now I am trying to perform a MD simulation, with the aim of obtaining a
stable structure, and begin the FEP simulation with this structure, but
I am finding SHAKE problems in performing the MD simulation.

My input file looks like

TBBNALA Escalfament
 &cntrl

  imin = 0, nmropt = 1,

  ntx = 1, irest = 0, ntrx = 1,
  ntxo = 1, ntpr = 1000,
  ntwx = 1000, ntwv = 0, ntwe = 1000,
  ioutfm = 0, ntwprt = 0, ntwr = 500,

  ntf = 2, ntb = 0, dielc = 1.0,
  cut = 9.0, nsnb = 10,
  scnb = 2.0, scee = 1.2, ipol = 0,

  ibelly = 0, ntr = 0,

  maxcyc = 500, ncyc = 5000, ntmin = 1,
  dx0 = 0.1, dxm = 0.5, drms = 0.0001,

  nstlim = 10000, t = 0.0, dt = 0.001,

  temp0 = 298.0, tempi = 0.0,
  ig = 71277, heat = 0.0,
  ntt = 1, dtemp = 0.0,
  tautp = 0.5, vlimit = 20.0,

  ntp = 0, pres0 = 1.0, comp = 44.6,
  taup = 0.5, npscal = 1,

  ntc = 2, tol = 0.00005,

 &end

 &wt
  type='END'
 &end

 &rst
  iat=10,117 r1=3.0, r2=5.0, r3=15.0, r4=17.0,
  rk2=10., rk3=10.0,
 &end

 &rst
  iat=30,125 r1=3.0, r2=5.0, r3=15.0, r4=17.0,
  rk2=10., rk3=10.0,
 &end

and in the lasts lines in the output file are:


     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 3 57 130 131

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


Can anybody help me in understanding the problem there is in this
simulation?
And has anybody any suggestion to solve this problem?

Thank you very much in advance

Itziar


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Sep 09 2003 - 12:53:02 PDT
Custom Search