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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>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
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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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>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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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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Received on Tue Dec 16 2014 - 15:00:02 PST
