no, that's not correct. when you use ntr=1, there is _no_ fitting
involved. it applies positional restraints just as normal ntr=1
simulations. the rmsmask specifies an rmsd calculation, but no fitting
is involved.
what you are doing is certainly reasonable, but you can't expect
it to match something where a best fit is done.
if you want tgtmd simulations with best-fitting, use the fitmask.
this doesn't work with ntr=1.
carlos
On 9/22/07, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
>
> Dear Carlos,
>
> Thanks for your reply, but I am not sure if what you say is right
> or not compared to what is written in the TMD part of the manual.
>
> What I have done in this simulation is, I put positional restraints to
> residues :1-2,8-11,17-18. According to the manual, the structure will be
> implicitly 'fitted' to this positional restraints (I assume that this
> 'fitting' is best-fitting). The targetted rmsd will be, then, calculated
> for the residues :3-7,12-16 (without doing any fitting). That is what I
> wanted to do; first best-fit the structure to residues :1-2,8-11,17-18,
> then calculate the targetted rmsd for residues :3-7,12-16.
>
> The restraint weight is good enough for the system; I put this positinal
> restraints to the terminal base pairs so that the structure will not fall
> apart during the simulation.
>
> The way I see this simulation is as follows: With these restraints, the
> structure changes according to Newtonian Mechanics. At each step, energy
> information is calculated. Also, at each step, the structure is
> best-fitted to the reference structure according to restraintmask. Then,
> the targetted rmsd is calculated between the reference structure and
> the current MD structure for the atoms defined in tgtrmsmask (without
> doing any fitting). This information is written in the sander output file
> as "Current RMSD from reference". I dont think that the restraint weight
> is the reason why the sander output's targetted rmsds values are different
> than the ptraj's rmsd calculation.
>
> The ptraj script that I have is as follows:
> ----------------- ptraj.in ---------------------
> reference xray.inpcrd
> trajin tgtmd_1.traj
> rms reference :1-2,8-11,17-18
> rms reference out rmsd_out :3-7,12-16 nofit
> go
> ------------------------------------------------
>
> The problem arises in the analysis part. When I compare the ptraj output
> with the sander output ('Current RMSD from reference' rmsd values), they
> are different. Why are they different? I assumed that the alignment
> protocol for targetted MD is similar to ptraj's alignment protocol.
> If the methods used for the alignment is different, which result am I
> going to use; the ptraj's results or the sander output file results?
>
> If there is something wrong with the way I look at targetted MD, I
> will greatly appreciate your comments. Thanks.
>
> Best,
>
> On Sat, 22 Sep 2007, Carlos Simmerling wrote:
>
> > your restraint weight is very weak.
> > it will calculate the non-fit rmsd for atoms in
> > the rmsmask, but will do no best fit.
> > when you use ptraj and do an alignment, then
> > you already have something different from what
> > you asked sander to do. try to use ptraj to calculate
> > the rmsd without any fitting at all.
> > alternatively, use a much stronger restraint
> > weight and see if the agreement in rmsd improves.
> > it could be something else, but I am guessing it
> > is the extremely weak restraint in sander as compared
> > to actual alignment in ptraj.
> >
> > On 9/22/07, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:
> > >
> > > Dear Amber Users,
> > >
> > > I am having trouble understanding how the RMSD is calculated in
> targetted
> > > MD simulations. I have the following input file:
> > > ------------ tgtmd.in ------------------------
> > > TMD: NMR->XRAY; target rmsd 3.267; resid 1-2,8-11,17-18 restrained
> > > &cntrl
> > > imin = 0, ntx = 5, nstlim = 1200000, irest=1,
> > > dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
> > > tempi = 300.0, temp0 = 300.0,
> > > scee = 1.2, cut = 99.9,
> > > ntpr = 50, ntwx = 50, ntwr = 50,
> > > ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
> > > igb = 1, nscm = 0, nmropt = 0,
> > > ntr = 1, restraint_wt=0.02,
> > > restraintmask=":1-2,8-11,17-18",
> > > itgtmd = 1, tgtrmsd = 3.267, tgtmdfrc = 1.0,
> > > tgtrmsmask="(:3-7,12-16)",
> > > /
> > > -----------------------------------
> > > What this script does is it restraints the residues 1-2,8-11,17-18
> > > with a restraint weight of 0.02. While doing that, implicitly, it
> aligns
> > > the system with respect to restraintmask.
> > >
> > > Then, the rmsd is calculated for the residues 3-7,12-16. At each
> > > step, "Current RMSD from reference" is printed out. I could not figure
> out
> > > how this 'Current RMSD from reference' is calculated. When I extract
> that
> > > particular snapshot from the trajectory and use ptraj (first aligning
> the
> > > residues 1-2,8-11,17-18 and then calculating the rmsd of residues
> > > 3-7,12-16), I get pretty different result.
> > >
> > > 1. Is there a mistake the way I describe/understand the above input
> file?
> > > 2. Does TMD follow a different alignment algorithm?
> > >
> > > Thanks in advance for your responses.
> > >
> > > Best,
> > >
> > > --
> > > Ilyas Yildirim
> > > ---------------------------------------------------------------
> > > = Department of Chemistry - =
> > > = University of Rochester - =
> > > = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> > > = http://www.pas.rochester.edu/~yildirim/ =
> > > ---------------------------------------------------------------
> > >
> > >
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> > >
> >
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Chemistry - =
> = University of Rochester - =
> = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
>
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--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
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Received on Sun Sep 23 2007 - 06:08:04 PDT
