RE: AMBER: Questions about sander.QMMM

From: Ross Walker <>
Date: Fri, 7 Jan 2005 11:38:29 -0800

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
> 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

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Fri Jan 07 2005 - 19:53:00 PST
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