Hello Ibrahim;
If you are interested in getting normal modes and corresponding PCA pdb
then use VMD. Add ProDy plugin in PDB. Upload your stripped MD coordinate
and stripped topology/stripped pdb. Go to Normal Mode Wizard>Run
PCA>specify the path for ProDy and thats it you will get porcupine plots
and motion direction in that and you can save corresponding PDB with motion
direction embedded in it.
Best;
SB
On Tue, May 27, 2014 at 10:39 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Tue, May 27, 2014 at 2:32 PM, Ibrahim Said <saidibrahim569.gmail.com>
> wrote:
> > Dear/ Roe DR
> > Thank you. Please can give me more details for this command. In other
> > words, How can get parm topology.parm7
>
> 'parm' is a command which loads a topology file; in this case you
> should use whatever topology you were using when you performed the
> original PCA. 'readdata' reads in a data set, in this case the
> eigenmodes you previously calculated with 'diagmatrix' (or 'analyze
> matrix').
>
> Note that the 'pcmin' etc. keywords are part of the 'modes' analysis
> command and should be on the same line, or should have a continuation
> (backslash, '\'), e.g.
>
> modes name evecs.dat trajout PC1.nc trajoutfmt netcdf \
> trajoutmask .CA pcmin <X> pcmax <Y> trajmode 1
>
> One last note - the mask given to 'trajoutmask' should be the same one
> you used in generating the covariance matrix. The Amber 14 manual has
> more details on these commands/keywords.
>
> Good luck,
>
> -Dan
>
> >
> > Thank you again,
> >
> > said
> >
> >
> >
> > On Tue, May 27, 2014 at 3:49 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> You can generate pseudo-trajectories of motion along specific
> >> eigenvectors with the 'modes' analysis command in cpptraj, e.g.
> >>
> >> parm topology.parm7
> >> readdata evecs.dat
> >> modes name evecs.dat trajout PC1.nc trajoutfmt netcdf trajoutmask .CA
> >> pcmin <X> pcmax <Y> trajmode 1
> >>
> >> will generate a pseudo-trajectory called PC1.nc in netcdf format along
> >> the first principle component from evecs.dat ranging from PC
> >> projection values of <X> to <Y>. The best way to determine appropriate
> >> values for <X> and <Y> are to look at the distribution of principle
> >> component projection values via the 'projection' command.
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >> On Mon, May 26, 2014 at 12:54 PM, Ibrahim Said <
> saidibrahim569.gmail.com>
> >> wrote:
> >> > Dear Amber users
> >> > I carried out a molecular dynamics simulation of a protein for 5 ns
> and
> >> > then I calculated the PCA for these trajectories and get the file for
> 15
> >> > projections. Now I don't know how can I get 15 pdb files
> corresponding to
> >> > these projections. Please, can someone help me to get these pdbs.
> >> >
> >> > Kind Wishes,
> >> >
> >> > Said
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> 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
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed May 28 2014 - 01:30:03 PDT
