On Wed, 2015-01-28 at 11:41 +0530, Pallavi Mohanty wrote:
> 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
24.7 Angstroms?? This seems too large, and I would recommend
double-checking this.
> 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.
If you look at the output file, you see that the restraint energy is
very large and the temperature shoots up within 30 steps (ca. 60 fs)
before you get a SHAKE failure.
This tells you that your simulation has blown up. Given that your force
constant is so small, I think this is further evidence that the target
RMSD (24.7) is not right.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 28 2015 - 05:30:03 PST
