I forgot to mention that cpptraj has the ability to output a normal
mode wizard-compatible file from the 'diagmatrix' analysis command,
e.g.:
diagmatrix mycovar_matrix out evecs.dat vecs 5 nmwiz nmwizvecs 5 \
nmwizfile nmwiz.nmd nmwizmask <matrix mask>
will generate nmwiz.nmd (compatible with VMDs normal mode wizard
plugin) containing 5 eigenvectors from diagonalization of covariance
matrix mycovar_matrix; <matrix mask> is an atom mask corresponding to
the one used to generate the covariance matrix.
Hope this helps,
-Dan
On Wed, May 28, 2014 at 2:08 AM, Soumendranath Bhakat
<bhakatsoumendranath.gmail.com> wrote:
> 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
> _______________________________________________
> 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
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Received on Wed May 28 2014 - 07:00:03 PDT
