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
Received on Sat Dec 13 2014 - 20:30:02 PST
