I can't say exactly what's wrong here without a lot more info (such as how
you equilibrate, the initial rmsd, the restraint energies vs time, what you
mean by "mutant" etc) , but I suspect in the end it's that what you're
trying to do won't really work. It looks like you want to use tmd to bring
it from 30A to 1A. You'll need to look at the rmsd vs time and see if it is
actually working. I would not expect it to. You'll probably reduce the rmsd
some and get into a compact state where rmsd restraints won't be able to
force the protein along a productive folding path. Once the atoms are
packed, the energies will just start going up because of stearic clashes.
Even if this is not the cause of your energy rise, I expect it to happen
and I dont think your simulations will do what they appear to be designed
to do.
I think you need to reconsider your goals and try to find examples where
simulations have worked for similar problems, and try those methods.
As an aside, I suggest not using igb=1 for proteins, but I don't know what
force field you are using so it's hard to make suggestions.
On Aug 19, 2016 3:06 AM, "Aravind Ravichandran" <raravind.ibab.ac.in> wrote:
> Dear AMBER users,
> I had performed a Targeted MD simulation for my mutant protein.This is
> my input file -
>
> targeted MD . 20*c
> &cntrl
> imin = 0, nstlim = 30000, dt = 0.0007,
> ntx = 1, ntt = 0,
> ntc = 2, ntf = 2, ntb = 0,
> cut = 999.0,
> ntpr = 10, ntwx = 10, ntwr = 10,
> igb = 1, irest=0, nmropt=1,tempi=293.0,
> itgtmd=1, tgtrmsd=1 tgtmdfrc=1.00,
> tgtfitmask=":1-520.CA,N,C,O",
> tgtrmsmask=":1-520 & !.H=",
> /
> &wt
> TYPE='TGTRMSD', istep1 =1, istep2 = 30000,
> value1 = 30.6, value2 = 1.0,
> /
> &wt
> type="END",
> /
>
> I have set the temperature of the system at 293 K. But as TMD progress the
> temperature of the system shoots-up to 800K.
> Is it normal?
> Will the protein not get denatured at 800K?
> Is there any way to maintain temp constant?
> Why is there a temperature shoot-up?
> I have attached the graph of temperature along TMD with this mail.
>
> Thanking u in advance,
> Aravind R
>
> ======================================================================
> Aravind R
> Research Associate
> Institute of Bioinformatics and Applied Biotechnology
> Bangalore-560100
> ph-(+91)888-46-11-500
> ======================================================================
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Received on Fri Aug 19 2016 - 05:00:03 PDT
