I set nqt to 52. Now sander.QMMM really works.
Thanks Ross,
Jenk.
--- Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Jenk,
>
> > 1) I was wondering if it is possible to run
> > sander.QMMM using NOE restraints.
>
> As far as I can tell it should be possible although
> I haven't tested it with
> Amber 8.
>
> > However, I encountered a problem when
> > I tried to run sander.QMMD with the following
> > 300K constant temp QMMM
> > &cntrl
> > imin=0, ntb=0, pencut=-0.001,
> > cut=20, fcap=1.5,
> > tempi=0, temp0=300.0,
> > ntt=3, gamma_ln=10, vlimit=10,
> > nstlim=1000, dt=0.001,
> > ntpr=10, ntwx=10, nmropt=1,
> > ifqt=1, nqt=12, idc=0,
> > /
> > 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
> > 16 17 18 19 20 21 22 23 24 25 26 27
> > 28 29 30 31 32 33 34 35 36 37 38 39
> > 40 41 42 43 44 45 46 47 48 49 50 51
> > 52
>
> What is the nqt=12 flag?
> This is your problem I suspect. You have specified
> only 12 quantum atoms in
> your second run. Although you still specify 52
> numbers. Having 12 atoms in
> your QM system the second time has changed the
> number of link atoms. Hence
> when the code reads in the restrt file from your
> minimisation it doesn't
> find enough link atoms and so gives you the error
> message you see below.
>
> Number of triangulated 3-point waters found:
> 400
> > FATAL ERROR
> > Link atoms MUST be optimized before MD run
>
> Try re-running with nqt=52. Also make sure you are
> reading the restrt file
> from the previous QM calculation so that it picks up
> the minimised position
> of the link atoms.
>
> > 2)Is it a good idea to incorporate NOE restraints
> > during
> > QMMM runs for solvated systems? Would it be a
> better
> > idea
> > to NMR restrain my molecule in implicit water
> first,
>
> QMMM in Amber 8 doesn't work with implicit solvent.
> Amber 9 hopefully will
> but for the moment you are restricted to classical
> simulations for implicit
> solvent. Your choice of method really depends on how
> far your system is from
> equilibibrium. If it is a long way then you could
> run a classical
> minimisation and some classical MD in solvent and
> then switch to running
> QMMM minimisation and MD. However, if you starting
> structure is pretty good
> you should just be able to run QMMM minimisation and
> MD from the offset. You
> may need to apply weak harmonic restraints (ntr=1)
> on the solute for the
> first stage of the MD to allow the water to relax an
> then slowly remove
> these restraints so your entire system can relax.
> Note, with QMMM MD it is
> often necessary to use a short time step, say 0.5fs
> to avoid instability.
>
> > then
> > take the final structure of my molecule, solvate
> it
> > and run
> > sander.QMMM putting a restrain for the final
> > structure?
>
> Are the restraints an important part of your
> simulation? What exactly are
> you trying to do?
>
> > 3) Is it possible to score final QMMM structures
> using
> > mm_pbsa?
> > As far as I understand from the QMMM tutorial
> (2004),
> > a solvatebox
> > is not added in prmtop files. I have tried running
> > mm_pbsa for an
> > QMMM coordinate output, however, mm_pbsa was
> unable to
> > execute pbsa.
> > Do I need to define a solvatebox in my prmtop file
> > while running
> > sander.QMMM so that mm_pbsa will be ok with
> > sander.QMMM output.
>
> I really don't know here, perhaps an mmpbsa person
> will know. The issue is
> that Amber 8 QMMM doesn't support periodic
> boundaries so you have to use a
> solvent cap with stochastic boundaries. Amber 9 QMMM
> will support periodic
> boundary QMMM simulations.
>
> I hope this helps
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:-
> ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available
> on request |
>
> Note: Electronic Mail is not secure, has no
> guarantee of delivery, may not
> be read every day, and should not be used for urgent
> or sensitive issues.
>
>
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Received on Sat Jan 08 2005 - 10:53:01 PST
