Hi Daniel,
I get the following error. earlier< i had rms fit based in the avg
structure. ans stored the coordinates.
I used this trajecory to run the commands as follows.
-----------------------input sequence--------------------------------
trajin 50ns_onlyavg_CAlpha.nc 1 100 1
matrix covar name covmat out covmat-ca.dat .CA
analyze matrix covmat name mymodes out evecs-ca.dat vecs 5
run
projection evecs mymodes myproj 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
--------------------------error message as follows-------------------
Read 10 frames and processed 10 frames.
ACTION OUTPUT:
DATASETS:
2 data sets:
covmat "covmat" (matrix), size is 696789
mymodes "mymodes" (modes), size is 0
ANALYSIS: Performing 1 analyses:
0: [analyze matrix covmat name mymodes out evecs-ca.dat vecs 5]
DATASETS AFTER ANALYSIS:
2 data sets:
covmat "covmat" (matrix), size is 696789
mymodes "mymodes" (modes), size is 5
DATAFILE OUTPUT:
covmat-ca.dat: covmat
covmat-ca.dat: Writing 2D data.
[projection evecs mymodes myproj out pca12-ca beg 1 end 2 .CA]
Error: projection: no modes file specified ('modes <filename>')
Error: Could not initialize action [projection]
-------------------------------------------------------
Best
Bergy
On Sat, Dec 13, 2014 at 9:26 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> A few suggestions here.
>
> On Sat, Dec 13, 2014 at 7:45 PM, BERGY <nucleic81.gmail.com> wrote:
> > trajin prod_50ns.nc
> > matrix covar name covmat out covmat-ca.dat .CA
>
> You probably want to remove overall rotational and translational
> motion here with something like an RMS fit to an average structure
> first, otherwise your matrix will include contributions from these
> motions. This may be contributing to the high projection values you
> are seeing.
>
> > Error: Could not initialize action [projection]
>
> When you enter commands they by default go into "lists" (e.g. the
> Action list or Analysis list), and are executed only when 'run' or
> 'go' is specified. You need to generate the eigenvectors before you
> project on them, therefore you want something like:
>
> matrix covar name covmat out covmat-ca.dat .CA
> analyze matrix covmat name mymodes out evecs-ca.dat vecs 2
> run
> projection evecs mymodes myproj 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
>
> Note the comma between the data set argument (e.g. myproj:1) and the
> histogram dimensions. Alternatively you can specify dimensions with
> the min, max, and bins keywords.
>
> Hope this helps,
>
> -Dan
>
> >
> >
> > 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
> >>
> >
> > _______________________________________________
> > 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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Received on Tue Dec 16 2014 - 13:30:02 PST
