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
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--
-------------------------
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)
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Received on Tue May 27 2014 - 07:00:04 PDT
