Dear/ Roe DR
Thank you. Please can give me more details for this command. In other
words, How can get parm topology.parm7
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
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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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>
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Received on Tue May 27 2014 - 14:00:02 PDT
