Can you rerun without the nofit keyword?
Hai
On Tue, Oct 3, 2017 at 5:05 PM Sonia Ziada <sonia.ziada.gmail.com> wrote:
> Dear Carlos,
>
> Thank you for your reply.
>
> - I am writing the trajectory (netcdf file) and the mdout every 2 steps
> (ntwx=2 and ntpr=2), so the structures used in cpptraj should correspond
> exactly to those in the MD run.
> - I am sure that the reference used for the fitting in the MD run is the
> same that those I use in cpptraj
> - I have also checked that the masks are correct (by looking at: the header
> of the mdout, the output of cpptraj and by using ambmask program)
> - Finally, I have a looked at the ene.F90 sander script containing the
> subroutine fitrms (that calcutes the current rmsd after the fitting step)
> to ensure that the rmsd is mass weighted.
>
> I do not understand the difference in rmsd values between cpptraj and the
> mdout file. By calcutating the rmsd with cpptraj, I assumed that the
> alignment algorithm is the same in cpptraj as in sander. But is this true?
>
>
> *ZIADA Sonia*
> PhD Student, Structural Bioinformatics & Chemoinformatics
> Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
> d'Orléans 7311
> Rue de Chartres, 45067 Orléans, France
> T. +33 238 419 939
>
> 2017-10-03 18:44 GMT+02:00 Carlos Simmerling <carlos.simmerling.gmail.com
> >:
>
> > are you certain that the structures that you are using in ptraj
> correspond
> > exactly to those in the MD run? for example, are you writing every step?
> > and are you using netcdf format instead of the low precision trajectory
> > files?
> >
> > On Tue, Oct 3, 2017 at 7:36 AM, Sonia Ziada <sonia.ziada.gmail.com>
> wrote:
> >
> > > Dear Amber users,
> > >
> > > I am having trouble understanding how the RMSD is calculated in
> targeted
> > MD
> > > simulations.
> > >
> > > I am using tgtfitmask (:Mask1) and tgtrmsmask (:Mask2).
> > > I try to reproduce the sander output's targeted rmsd results (those
> > > available in the mdout file: “current rmsd from reference”) using
> cpptraj
> > > with the following commands:
> > >
> > > ### cpptraj script ---------------------------------
> > > parm topo.top
> > > trajin traj.nc
> > > reference reference.rst
> > > rms reference :Mask1
> > > rms reference mass :Mask2 out rmsd.dat nofit
> > > run
> > > quit
> > > --------------------------------------------------------
> > >
> > >
> > > *But I get different results: *
> > > ### 1) From the .mdout file:
> > > Current RMSD from reference: 0.017
> > > Current RMSD from reference: 0.049
> > > Current RMSD from reference: 0.075
> > > Current RMSD from reference: 0.094
> > > Current RMSD from reference: 0.110
> > >
> > > ### 2) From cpptraj (rmsd.dat file)
> > > 1 0.0337
> > > 2 0.0630
> > > 3 0.0853
> > > 4 0.1027
> > > 5 0.1178
> > >
> > > As far as I can conclude with these results, the TMD's alignment sceme
> > > seems different from cpptraj's alignment sceme. How can I reproduce the
> > > rmsd of the mdout using cpptraj ?
> > > Thank you.
> > >
> > >
> > > *ZIADA Sonia*
> > > PhD Student, Structural Bioinformatics & Chemoinformatics
> > > Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université
> > > d'Orléans 7311
> > > Rue de Chartres, 45067 Orléans, France
> > > T. +33 238 419 939
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Tue Oct 03 2017 - 16:30:02 PDT
