On Mon, 2014-05-12 at 08:47 +0000, Valentina Romano wrote:
> Dear Amber users
>
> I am still having problems with the equilibration stage.
>
> My system is a complex of a protein kinase binds to the 6amino-purine.
> The whole system contains 247 residues.
>
> First of all, I minimized the solvent (water +ions) keeping the protein's heavy atoms frozen:
>
> &cntrl
> imin=1,
> maxcyc=1000,
> ntb=1,
> ntr=1,
> cut=10,
> restraint_wt = 10.0,
> restraintmask=':1-247.CA,C,O,N,H'
You are also freezing some H atoms here.
> /
>
> Afterwards, I wanted to run a short MD keeping frozen the protein's
> heavy atoms to relax solvent molecules before running a minimization
> of the whole system:
>
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> ig=-1,
> ntb=1,
> ntr=1,
> cut=10,
> ntc=2,
> ntf=2,
> tempi=300.0,
> temp0=300.0,
> ntt=3,
> gamma_ln=5.0,
> nstlim=15000, dt=0.001,
> ntpr=100, ntwx=100, ntwr=1000
> restraint_wt = 10.0,
> restraintmask=':1-247.CA,C,O,N'
>
> Sander immediately stops with the following error message:
>
> vlimit exceeded for step 2; vmax = 144.9409
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 1927 3834 3844
Look at atoms 3834 and 3844 of your system and see if anything weird is
happening there.
Also, set ntpr=1 and ntwx=1 (I would also suggest using ioutfm=1 to use
the NetCDF format trajectory). Then see if can find out what is
happening to those atoms over the first few steps (this is always good
advice for debugging these kinds of problems).
It's possible that your reference structure is too different from your
starting structure that it is introducing a very large force. So you
should also compare to the structure you're passing as "-ref" to make
sure this isn't happening.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 12 2014 - 05:00:03 PDT
