Hi,
you only need to specify reference structure once.
every time you specify rms, there would be a rms fit unless 'nofit' is
specified, and you could write out rms if 'out' is specified.
below lines would do: you specify the reference structure, rms fit trj to
reference structure basing on protein atoms, then output rms of ligand.
reference reference_structure.pdb
rms reference mass :1-289
rms reference mass out ligand_rmsd.dat :290 nofit
On Wed, Apr 28, 2010 at 10:57 AM, Yingjie Lin <linyj1984.gmail.com> wrote:
> Hi Carlos,
>
> Thanks for that tip!
> Do you mean I should do the following?
>
> reference reference_structure.pdb :1-290
> rms reference mass :1-289
> rms reference mass out ligand_rmsd.dat :290 nofit
>
> or:
> reference reference_structure.pdb :1-289
> rms reference mass :1-289
> reference reference_structure.pdb :290
> rms reference mass out ligand_rmsd.dat :290 nofit
>
>
> Yingjie
>
> On Apr 27, 2010, at 9:14 PM, Carlos Simmerling wrote:
>
> > do this in 2 steps. first, align the protein using an rms command and
> mask
> > for the protein.
> > then do another rms command, for the ligand only, but put "nofit" at the
> end
> > of the line.
> >
> >
> > On Tue, Apr 27, 2010 at 8:42 PM, Yingjie Lin <linyj1984.gmail.com>
> wrote:
> >
> >> Dear all,
> >>
> >> I've run 30ns simulation of a protein-ligand complex.
> >> The protein has 289 residues, and the 290th "residue" corresponds to the
> >> ligand.
> >>
> >> I am interested in checking how the ligand move in the simulation.
> >> To be more specific, I would like to calculate RMSD of the ligand with
> >> respect to the ligand in another file (named fileA.pdb).
> >>
> >> My script looks like this:
> >> =======
> >> trajin ../EQ/complex.1.trj.gz 1 1000 25
> >> trajin ../EQ/complex.2.trj.gz 1 1000 25
> >> ...
> >>
> >> center origin :1-290
> >> image origin center
> >>
> >> rms first mass out complex_rmsf_ca.dat .CA
> >>
> >> strip :291-119999999
> >>
> >> reference fileA.pdb :1-290
> >> rms reference mass out ligand_rmsf.dat :290
> >> ======
> >> I am not sure about the last two lines. Since I want to "align the
> protein
> >> and then calculate RMSD for the ligand",
> >> which of the following should I use?
> >> 'reference fileA.pdb :1-290'
> >> or 'reference fileA.pdb :1-289'
> >> or 'reference fileA.pdb :290'
> >>
> >>
> >> Thanks a lot!
> >>
> >> Yingjie
> >> _______________________________________________
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> >>
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Received on Wed Apr 28 2010 - 09:00:05 PDT
