Hi Daniel,
Thank u,
That solved my problem.
Best,
Bergy
On Tue, Dec 16, 2014 at 3:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> On Tue, Dec 16, 2014 at 2:23 PM, BERGY <nucleic81.gmail.com> wrote:
> > Error: projection: no modes file specified ('modes <filename>')
> > Error: Could not initialize action [projection]
>
> This error message is from an old version of cpptraj. Make sure you're
> using the latest version from AmberTools 14 (14.22).
>
> -Dan
>
> > -------------------------------------------------------
> >
> > 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)
> >> >>
> >> >> _______________________________________________
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> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
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> >> >
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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)
> >>
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> >>
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>
>
>
> --
> -------------------------
> 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 - 22:00:01 PST
