Thank you. I just sent another email. For some reason, I never saw a
response to this one. I will try this.
Nicole
On Sat, May 3, 2014 at 2:11 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You can generate histograms of the principal component projections (I
> think this may be what you want) using CPPTRAJ, e.g.:
>
> parm mytopology.parm7
> # Average the trajectory
> rms first $MASK
> average Avg.rst7 restart
> createcrd crd1
> run
> # Fit to average structure
> reference Avg.rst7.1
> crdaction crd1 rms reference $MASK
> # Calculate and diagonalize covariance matrix
> crdaction crd1 matrix covar $MASK name Covar
> runanalysis diagmatrix Covar out evecs.dat vecs $NVECS name Evecs
> # Now calculate projection for trajectory
> crdaction crd1 projection T1 modes Evecs beg 1 end $NVECS $MASK
> # Histogram projection
> runanalysis multihist T1 bins 100 normint out hist.agr
>
> Replace $MASK with the appropriate atom mask and $NVECS with the
> desired # of vectors.
>
> Hope this helps,
>
> -Dan
>
> On Fri, May 2, 2014 at 9:17 AM, Nicole Ippolito
> <ippolito.nicole89.gmail.com> wrote:
> > Dear Amber Users,
> >
> > Is there a way to generate the percent occupancy with principal component
> > analysis using ptraj?
> >
> > Thank you,
> >
> > Nicole
> > _______________________________________________
> > 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
>
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Received on Mon May 05 2014 - 09:00:02 PDT
