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 - 19:54:17 CDT

Dear Carlos,

Thanks again for your response. So, you say that I can use both
restraintmask and tgtfitmask in a targetted MD simulation, is that right?
I did not use tgtfitmask because in the manual it says that when ntr=1 is
set, the structures is implicitly fitted according to atoms specified in
restraintmask. Looks like that there is a mistake in this part of the
manual.

I just searched the amber mailing list, and saw that someone already
pointed out this. I wish I read it before running the simulations. Thanks
again.

Best,

On Sat, 22 Sep 2007, Carlos Simmerling wrote:

> 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_at_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_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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>
>
> 

-- 
  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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