Your frame0.pdb has only 75 atoms. (Is this accidentally truncated??) This
does not have any atom belong to your mask, :34-39.CA|:101-107.CA. So, it
does not make sense to calculate rmsd without the coordinates.
On Thu, May 13, 2010 at 4:30 PM, <map110.pitt.edu> wrote:
> Hi again,
>
> So I'm attaching my ptraj.in file as well as all the files associated with
> it. This is the command I used for ptraj:
>
> ptraj orig_nowat.top <ptraj.in> ptraj.out
>
> I should also have mentioned that my system is comprised of a 100 residue
> receptor and 7 residue peptide fragment ligand and the ligand extends the
> anti parallel beta sheet of the receptor upon binding.
> Essentially, we've taken the pdb file for the system (which is also our
> reference structure) and shifted the position of the ligand upwards by two
> hydrogen bonds. With the targeted md simulation we want to force the
> conformational change of our structure to the final state (the NMR
> structure). In order to do this, we thought that it would make sense to
> designate tgtfitmask to be the ligand CA atoms and the tgtrmsmask to be
> the ligand CA atoms and the CA atoms from the beta strand of the receptor
> which make up the binding interface. Hope this clarifies a few things.
>
> Thanks again!
>
> Maria
>
> > Hi,
> > You also need to provide your script for ptraj. I see your tgtfitmask
> and
> > tgtrmsmask are different. So, I suppose your ptraj script has multiple
> > rms
> > commands.
> >
> > On Thu, May 13, 2010 at 3:19 PM, <map110.pitt.edu> wrote:
> >
> >> Hi everyone,
> >>
> >> I'm trying to run a 2 ns targeted md simulation in which the rmsd of the
> >> protein structure from the reference structure is gradually reduced over
> >> time. In order to test my input files, I ran a 1 ps test simulation and
> >> found that there was a discrepancy between the "current RMSD from
> >> reference" given in the .out file and the actual rmsd between the
> >> reference structure and the outputted frame0.rst file (found using
> >> ptraj).
> >> Specifically, in frame0.out the rmsd is 5.124, compared to the actual
> >> rmsd
> >> of 3.28614.
> >>
> >> This is the command I used:
> >>
> >> mpiexec -n 8 nice -19 sander.MPI -0 -i md.in -o frame0.out -p
> >> complex.top
> >> -c eq3.rst -r frame0.rst -x frame0.crd -ref origmin.rst
> >>
> >> I'm also attaching all my input and output files. If anyone has an input
> >> on this problem it would be greatly appreciated.
> >>
> >> Thanks in advance for your help!!
> >>
> >> Maria
> >>
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Best,
> > InSuk Joung
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Best,
InSuk Joung
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Received on Thu May 13 2010 - 14:30:04 PDT
