Hi Jason,
Thank you very much for your ideas. I first considered the nmropt option
and found some literature that have used TargetedMD, but in those occasions
they had used it when there was a transition from eg: an intermediate
structure to a particular target structure. But in my instance, its
different coz I don't want such a transition but simply a localization
around a point that is mainly why I sought the advice of the AMBER forum
before carrying out my plan. If anyone of you in the AMBER forum and
specially you, Jason,felt frustrated in answering my question I would like
to apologize for the inconvenience caused.
Thank you very much for the time spent on my behalf from your super busy
schedule
Sajeewa Dewage
On Fri, Feb 1, 2013 at 10:11 PM, Jason Swails <jason.swails.gmail.com>wrote:
> It seems like a flat-well potential would suit better here. You can
> effectively use a distance restraint with a flat-well potential like a
> spherical well to keep the CO2 molecule inside a region of spaced defined
> with respect to the center of mass of a particular set of atoms.
>
> With a flat-well potential, you can make it so there is no penalty for
> staying within, say, 5 Angstroms of a given point in space (defined
> relative to your system, so this restraint is immune to
> translations/rotations, unlike, say, positional restraints). After this,
> the penalty becomes quadratic (and eventually linear). Look at the nmropt
> option (and NMR restraints in the manual).
>
> Targeted MD does not seem to be the right choice, in part because you are
> affecting your system a lot simply to keep the CO2 molecules localized.
> The flat-well potential is a far smaller perturbation (and it allows you
> to run with pmemd and pmemd.cuda, too).
>
> It is important to be able to defend what you are doing and anticipate ways
> in which your settings may affect the system and bias your results. Also
> think about what question you are asking and how your simulation will (or,
> even better, would NOT) work to answer that question. For instance, you
> can't design a simulation aimed at forcing CO2 to stay in a particular
> region inside the protein and then claim you've found the CO2 binding
> pockets.
>
> Ultimately, however, all of this is speculation. Nobody can answer these
> questions better than the simulations themselves, and I encourage you to
> allow some more time between repeats of the same email (and even consider
> that nobody may have the answer to your question). It will most likely
> only frustrate the people whose help you want.
>
> Good luck,
> Jason
>
> On Fri, Feb 1, 2013 at 5:59 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >wrote:
>
> > Hi all,
> >
> > I would be highly obliged if you could please look into this. I can run
> my
> > calculation with this set up and see what happens, I just wanted to get
> the
> > set up perused and may be get modified by your expertise.
> >
> > Thank you
> >
> > Sajeewa Dewage
> >
> > ---------- Forwarded message ----------
> > From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
> > Date: Thu, Jan 31, 2013 at 1:03 PM
> > Subject: Sampling of a point by a molecule while keeping the relative
> > position of the molecule unchanged in TMD
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > Hi all,
> >
> > I have some CO2 molecules placed at particular , pre-determined points
> > inside a protein. I want to sample the positions of CO2 molecules around
> > those particular points while keeping their relative position with
> respect
> > to the surrounding of each CO2 as constant as possible. When I went
> through
> > the description of the technique in the AMBER manual I thought targeted
> MD
> > would serve the purpose coz it allows to give a set of atoms as a
> reference
> > and restrain the motion of the atoms, in terms of RMSD while the
> simulation
> > is going on.
> >
> > Letz say that the residue numbers that I use as surrounding for a
> > particular CO2 are 410, 385, 835, 525 and the residue number of the
> > particular CO2 is 902
> >
> > If I have an mdin file like below, will it serve my purpose(i.e to keep
> the
> > position of the residue 902 more or less constant with respect to the
> > surrounding while having my initial protein.prmcrd file as the reference
> in
> > *-ref*)?
> >
> > TMD
> > &cntrl
> > ntx=1,irest=0,
> > nsnb=1,ntpr=5,ntwx=100,nstlim=500000,dt=0.001,
> > ntc=2,ntf=2,ntb=1,iwrap=1,
> > ntt=3,temp0=300,tempi=300,gamma_ln=4,ig=10502,
> > cut=8.0,
> > igtmd=1,tgtfitmask=':410,385,835,525,902',
> > tgtrmsmask=':410,385,835,525,902', tgtrmsd=0.0, tgtmdfrc=1.0,
> > /
> >
> > Please suggest if any modifications are required. And about the force
> > constant(tgtmdfrc=1.0), should I apply a higher force constant? If so
> like
> > how much?
> >
> > Thank you very much
> >
> > Sajeewa Dewage
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Feb 01 2013 - 21:30:02 PST
