AMBER Archive (2007)

Subject: Re: AMBER: TMD and "Current RMSD from reference"

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sat Sep 22 2007 - 15:49:26 CDT

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_at_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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