Date: Sat, 13 Dec 2014 19:45:17 -0700
Thanks for ur quick reply,
----------------
trajin prod_50ns.nc
matrix covar name covmat out covmat-ca.dat .CA
analyze matrix covmat out evecs-ca.dat vecs 2
projection modes evecs-ca.dat out pca12-ca beg 1 end 2 .CA
---------------
The above script gives me the 2d project. but when i try to add line for
hist cal I get error msg
-----------------
trajin prod_50ns.nc
matrix covar name covmat out covmat-ca.dat .CA
analyze matrix covmat out evecs-ca.dat vecs 2
projection modes evecs-ca.dat out pca12-ca beg 1 end 2 .CA
hist myproj:1 -60,60,*,360 free 300 out PC.hist.agr
hist myproj:2 -60,60,*,360 free 300 out PC.hist.agr
go
-------ERROR OUTPUT-------
CPPTRAJ: Trajectory Analysis. V13.24
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
Warning: Topology: Input bonds and bondsh are empty.
INPUT: Reading Input from file pca4.ptraj
[trajin 50ns_EF-Tu_GDP_wat_md3_combined_centered_CAonlyavg.nc]
[50ns_EF-Tu_GDP_wat_md3_combined_centered_CAonlyavg.nc] contains
25000 frames.
Warning: Box information present in parm but not in trajectory.
Warning: DISABLING BOX in parm
[onlyCA_striped.stripped.EF_Tu_GDP_399_WAT.prmtop]!
[matrix covar name covmat out covmat-ca.dat .CA]
MATRIX: Calculating covar matrix, output is by atom
Printing to file covmat-ca.dat
Storing matrix on internal stack with name: covmat
Start: 1 Stop: Final frame
Mask1: .CA
[analyze matrix covmat out evecs-ca.dat vecs 2]
ANALYZE MATRIX: Analyzing matrix covmat and dumping results to
evecs-ca.dat
Calculating 2 eigenvectors
[projection modes evecs-ca.dat out pca12-ca beg 1 end 2 .CA myproj]
Error: Could not initialize action [projection]
Also , While doing PCA
I see that in my 2dproj the unit are ver high-40 ,+60, is it unusual?
See fIgure attached.
On Sat, Dec 13, 2014 at 4:48 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> On Sat, Dec 13, 2014 at 3:39 PM, BERGY <nucleic81.gmail.com> wrote:
> > I am not sure ho the what energy is plotted .How it should be calculated?
>
> These are free energies calculated from histogram bin populations,
> i.e. the free energy of bin i, dGi is:
>
> dGi = -RT * ln(popi)
>
> where popi is typically the population of bin i divided by the
> population of the most populated bin (making your free energy minimum
> always 0). This can be done with the cpptraj command 'hist' and the
> keyword 'free <temperature>'. However, be aware that your data needs
> to be fairly well converged in order to get accurate estimates of free
> energy this way. You'll typically need at least 2 independent
> simulations starting from different initial conditions to really
> assess convergence.
>
> > For now I have done
> > aligning all the trajectories to the average structure and then calculate
> > the
> > projections.
> > -------------
> > matrix covar name covmat out covmat-ca.dat .CA
> > analyze matrix covmat out evecs-ca.dat vecs 2
> > projection modes evecs-ca.dat out pca12-ca beg 1 end 2 .CA
> > ------------
> > Tthe two averages from each of the two simulation our different..
> > Can I compare the two 2D projections?
>
> Maybe. When you perform PCA for each trajectory separately there is no
> guarantee that the eigenvectors from each are the same; odds are they
> will differ at least by a little, and maybe by a lot. You would have
> to calculate the angle between each eigenvector to see how
> well-aligned they are. A better approach in my opinion is to generate
> the covariance matrix from all of your trajectories, then project
> along the eigenvectors for each trajectory separately. For some
> examples of this approach see some recent work from our lab (and the
> supplementary information therein.):
>
> http://www.sciencedirect.com/science/article/pii/S0304416514003092
> http://pubs.acs.org/doi/abs/10.1021/jp4125099
> http://pubs.acs.org/doi/abs/10.1021/ct400862k
>
> > If I have xtal.pdb , how to get the 2p for that structure and overlay on
> > the 2D projection plot?
>
> If I understand your question correctly, you need to project the PDB
> coordinates along your calculated eigenvectors. The trick is ensuring
> the atoms in the crystal PDB have the same ordering as the topology
> you used to calculate your covariance matrix. Your best bet for that
> is to just use the initial structure and topology you got from tleap,
> prior to minimization.
>
> Hope this helps,
>
> -Dan
>
> >
> > Thanks in advance.
> >
> > Best,
> > Bergy
> > _______________________________________________
> > 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 307
> 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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(image/png attachment: pca.png)
