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
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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 Sat May 03 2014 - 00:30:02 PDT
