On Wed, Jan 28, 2015, Pallavi Mohanty wrote:
> 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,
Did the error happen on the first step, or part way into the simulation?
Try turning off targetted MD and see if the error goes away. Look at the
energy and forces at the first few steps; you might want to visualize
the trajectory (set ntwx=1). Try making the tgtmdfrc much smaller.
As an aside, for proteins we strongly recommend using ff14SBonlysc and igb=8.
See
%A H. Nguyen
%A J. Maier
%A H. Huang
%A V. Perrone
%A C. Simmerling
%T Folding Simulations for Proteins with Diverse Topologies Are Accessible in
Days with a Physics-Based Force Field and Implicit Solvent
%J J. Am. Chem. Soc.
%V 136
%P 13959-13962
%D 2014
What you get with igb=1 dates back to the previous millenium, and this is a
fast-moving field.
...good luck...dac
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Received on Wed Jan 28 2015 - 05:00:07 PST
