AMBER Archive (2007)

Subject: AMBER: Deep energetics problem

From: sai vikram (vsaivikram_at_gmail.com)
Date: Tue Jan 02 2007 - 11:10:19 CST

Hi,

I am trying to do a NPT simulation with a protein structure restraining

Restrain 2 to 20 residues

1.0

Restrain the CA atom of first residue strongly

1.0

Before this particular run i carried out a minimization amd Simulated
annealing step with restrains.

  50.0
 RES 2 20
 Restrain the CA atom of first residue strongly
 1000.0

I wish my system should be at constant pressure 200.0 .

*******************************************************************************

Error:

vlimit exceeded for step 6; vmax = 59.1247

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 78 140 141

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

*******************************************************************************

I have tried to search in google and read the messages posted previously
by others, and reduced the restraints as per their suggestions. Yet, i could
not able to run my system
$ Can someone please advice me here. below is my input file

Input file is
--------------------------------------------------------------------------------------------------------------------
 &cntrl
  imin = 0, ntx = 7, irest = 1,
  ntpr = 100, ntwx = 500, ntwe = 0, ntwprt=0,
  ntc = 2, ntf = 2,
  nstlim = 50000, dt =0.002,
  tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
  ntb = 2, ntp = 1,taup=0.2, pres0=200.0,
  ntr=1,iwrap=1,cut=10.0
 &end
 Restrain the heavy atoms
 1.0
 RES 2 20
END
 Restrain the CA atom of first residue strongly
 1.0
 FIND
 * CA * *
 SEARCH
 RES 1
END
END

Amber Version : 9

Operating System : Linux

--------------------------------------------------------------------------------------------------------------

Thanks in advance,

-Vikram

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