The coordinates of frame0.pdb is same as those of frame0.rst. So, I assume
the pdb is from the restart file. In your md input, ntwr=1000 and ntpr=500,
which means that frame0.rst corresponds to the output of NSTEP=1000 and the
rmsd is 5.006. So your rmsd calculated using ptraj should be same as this
number.
Now, in you ptraj input, I see only single line of rms command.
It should be
trajin frame0.pdb
reference origmin.pdb
rms reference :101-107.CA mass
rms reference out rmsd.dat (:34-39.CA|:101-107.CA) nofit mass
Please be careful about the second rms command. It has nofit. In the first
rms command above, your molecule is fitted using the mask, :101-107.CA. In
the second rms command, rmsd is calculated without FITTING! That is what
you meant in your md input file ( tgtfitmask=":101-107.CA",
tgtrmsmask="(:34-39.CA|:101-107.CA)" ) Also, you should not forget mass
because targeted md does mass-weighted fitting.
By doing so, I got 5.005 for rmsd. I believe the difference by 0.001 is due
to the truncated coordinates of the pdb file.
I hope it is clear to you.
On Fri, May 14, 2010 at 11:05 AM, <map110.pitt.edu> wrote:
> Hi there,
>
> I'm not sure why that happened. I'm attaching frame0.pdb again but it's
> the complete file. This is what I used for ptraj. I'm also attaching my
> ptraj.out file.
>
> Thanks!
>
> Maria
>
> > 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
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Best,
> > InSuk Joung
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Best,
InSuk Joung
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Received on Fri May 14 2010 - 09:30:04 PDT
