[AMBER] Targeted MD error

From: Pallavi Mohanty <pallavipmohanty.gmail.com>
Date: Wed, 28 Jan 2015 11:41:21 +0530

Dear Users,
I am running TMD in AMBER, at this point i am done with heating and
equilibration steps. I have an open and closed conformation and i want to
span the transition from open to closed.The Basic difference between both
the structure is the first helix that moves out and has an RMSD of 24.7 for
1-37 residues

My Input file for TMD was

TMD: open->closed; target rmsd 1.6; resid 38-134 restrained TMD:
open->closed; target rmsd 1.6; resid 38-134 restrained
 &cntrl
      imin = 0, ntx = 5, nstlim = 5000, irest = 1,
      dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
      temp0 = 300.0,
      cut = 16.0,
      ntpr = 1, ntwx = 50, ntwr = 500,
      ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
      igb = 1, nscm = 0, nmropt = 1,
      ntr = 1, restraint_wt = 0.02,
      restraintmask = ":38-134",
      itgtmd = 1, tgtrmsd = 24.7, tgtmdfrc = 1.0,
      tgtrmsmask = "(:1-37)",
      /
 &wt
      TYPE='TGTRMSD', istep1=1, istep2=1000,
      value1 = 1.000, value2 = 0.0,
 /
 &wt
      TYPE='TGTRMSD', istep1=1000, istep2=0,
      value1 = 0.0, value2 = 0.0,
 /
 &wt
    type='END',
/
and I got an error stating
"Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 428 826 827

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system."
Have attached the out file too!
Please suggest where I have gone wrong.

-- 
Regards,
Pallavi Mohanty



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Received on Tue Jan 27 2015 - 22:30:05 PST
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